Starting phenix.real_space_refine on Fri Aug 7 04:10:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igw_52860/08_2026/9igw_52860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igw_52860/08_2026/9igw_52860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9igw_52860/08_2026/9igw_52860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igw_52860/08_2026/9igw_52860.map" model { file = "/net/cci-nas-00/data/ceres_data/9igw_52860/08_2026/9igw_52860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igw_52860/08_2026/9igw_52860.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 P 264 5.49 5 S 40 5.16 5 C 11101 2.51 5 N 3404 2.21 5 O 4103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18912 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 634 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "K" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3641 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 218 Chain: "L" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3960 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 9, 'HIS:plan': 2, 'TYR:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 160 Chain: "I" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2687 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2725 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Time building chain proxies: 4.62, per 1000 atoms: 0.24 Number of scatterers: 18912 At special positions: 0 Unit cell: (173.34, 131.61, 120.91, 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 40 16.00 P 264 15.00 O 4103 8.00 N 3404 7.00 C 11101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 738.9 milliseconds 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 51.9% alpha, 11.9% beta 100 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.981A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.781A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.395A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.507A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.781A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.414A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.724A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 45 through 50 removed outlier: 4.008A pdb=" N PHE K 49 " --> pdb=" O SER K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 58 through 78 Processing helix chain 'K' and resid 112 through 122 removed outlier: 4.023A pdb=" N PHE K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 135 Processing helix chain 'K' and resid 142 through 156 Processing helix chain 'K' and resid 180 through 196 removed outlier: 3.662A pdb=" N THR K 196 " --> pdb=" O ASP K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 312 through 314 No H-bonds generated for 'chain 'K' and resid 312 through 314' Processing helix chain 'K' and resid 330 through 339 Processing helix chain 'K' and resid 354 through 356 No H-bonds generated for 'chain 'K' and resid 354 through 356' Processing helix chain 'K' and resid 377 through 393 removed outlier: 3.781A pdb=" N LEU K 381 " --> pdb=" O GLY K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 455 through 469 Processing helix chain 'K' and resid 480 through 495 removed outlier: 3.525A pdb=" N GLN K 484 " --> pdb=" O ASN K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 519 Processing helix chain 'K' and resid 520 through 530 Processing helix chain 'L' and resid 29 through 48 removed outlier: 3.779A pdb=" N LYS L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 97 Processing helix chain 'L' and resid 106 through 123 Processing helix chain 'L' and resid 146 through 157 Processing helix chain 'L' and resid 198 through 217 Processing helix chain 'L' and resid 218 through 220 No H-bonds generated for 'chain 'L' and resid 218 through 220' Processing helix chain 'L' and resid 226 through 232 removed outlier: 3.785A pdb=" N ARG L 232 " --> pdb=" O SER L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 331 Processing helix chain 'L' and resid 370 through 388 Processing helix chain 'L' and resid 447 through 461 Processing helix chain 'L' and resid 484 through 500 removed outlier: 4.404A pdb=" N GLN L 488 " --> pdb=" O ASN L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 517 removed outlier: 3.913A pdb=" N TRP L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 537 removed outlier: 4.200A pdb=" N THR L 523 " --> pdb=" O PRO L 519 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE L 528 " --> pdb=" O THR L 524 " (cutoff:3.500A) Proline residue: L 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.270A pdb=" N ARG A 84 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.632A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.284A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.692A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.883A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.518A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.425A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 102 through 109 removed outlier: 8.163A pdb=" N LEU K 105 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N PHE K 87 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU K 107 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL K 85 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER K 37 " --> pdb=" O ARG K 165 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N MET K 167 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE K 39 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N PHE K 169 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU K 41 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS K 164 " --> pdb=" O PHE K 199 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP K 201 " --> pdb=" O LYS K 164 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE K 166 " --> pdb=" O ASP K 201 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET K 203 " --> pdb=" O ILE K 166 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU K 168 " --> pdb=" O MET K 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 257 through 262 removed outlier: 3.831A pdb=" N PHE K 432 " --> pdb=" O VAL K 368 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N VAL K 394 " --> pdb=" O PRO K 415 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA K 395 " --> pdb=" O PHE K 350 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE K 350 " --> pdb=" O ALA K 395 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU K 397 " --> pdb=" O MET K 348 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET K 346 " --> pdb=" O ARG K 399 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU K 345 " --> pdb=" O LYS K 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 286 through 288 Processing sheet with id=AB4, first strand: chain 'K' and resid 296 through 304 removed outlier: 3.505A pdb=" N GLU L 292 " --> pdb=" O ARG K 301 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR L 295 " --> pdb=" O VAL L 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 326 through 329 Processing sheet with id=AB6, first strand: chain 'L' and resid 77 through 84 removed outlier: 4.710A pdb=" N VAL L 79 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU L 58 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU L 83 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE L 54 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA L 8 " --> pdb=" O GLU L 53 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA L 55 " --> pdb=" O ALA L 8 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL L 10 " --> pdb=" O ALA L 55 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL L 57 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU L 12 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE L 59 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA L 9 " --> pdb=" O HIS L 131 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU L 133 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL L 11 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE L 135 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER L 160 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE L 164 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 247 through 253 removed outlier: 7.306A pdb=" N VAL L 361 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLN L 360 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN L 423 " --> pdb=" O GLN L 360 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU L 362 " --> pdb=" O TYR L 421 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ALA L 366 " --> pdb=" O GLU L 417 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N GLU L 417 " --> pdb=" O ALA L 366 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N MET L 389 " --> pdb=" O PRO L 410 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG L 394 " --> pdb=" O VAL L 342 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL L 342 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA L 396 " --> pdb=" O PHE L 340 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE L 340 " --> pdb=" O ALA L 396 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 239 hydrogen bonds 446 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4429 1.33 - 1.45: 4940 1.45 - 1.57: 9821 1.57 - 1.69: 526 1.69 - 1.81: 63 Bond restraints: 19779 Sorted by residual: bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" C3' DA J 43 " pdb=" C2' DA J 43 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I 85 " pdb=" C2' DC I 85 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J 83 " pdb=" C2' DG J 83 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J 117 " pdb=" C2' DT J 117 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 19774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 27075 2.03 - 4.06: 794 4.06 - 6.09: 40 6.09 - 8.12: 14 8.12 - 10.15: 3 Bond angle restraints: 27926 Sorted by residual: angle pdb=" O4' DG I 56 " pdb=" C4' DG I 56 " pdb=" C3' DG I 56 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.90e+01 angle pdb=" O4' DC I 144 " pdb=" C4' DC I 144 " pdb=" C3' DC I 144 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O4' DC I 25 " pdb=" C4' DC I 25 " pdb=" C3' DC I 25 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O4' DC I 71 " pdb=" C4' DC I 71 " pdb=" C3' DC I 71 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N LYS B 91 " pdb=" CA LYS B 91 " pdb=" C LYS B 91 " ideal model delta sigma weight residual 111.28 106.24 5.04 1.09e+00 8.42e-01 2.13e+01 ... (remaining 27921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 9766 35.32 - 70.64: 1475 70.64 - 105.95: 60 105.95 - 141.27: 2 141.27 - 176.59: 5 Dihedral angle restraints: 11308 sinusoidal: 6137 harmonic: 5171 Sorted by residual: dihedral pdb=" CA GLN L 73 " pdb=" C GLN L 73 " pdb=" N TYR L 74 " pdb=" CA TYR L 74 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 95 " pdb=" C3' DG I 95 " pdb=" O3' DG I 95 " pdb=" P DC I 96 " ideal model delta sinusoidal sigma weight residual 220.00 43.41 176.59 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 72 " pdb=" C3' DG I 72 " pdb=" O3' DG I 72 " pdb=" P DC I 73 " ideal model delta sinusoidal sigma weight residual 220.00 54.80 165.20 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 11305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2514 0.049 - 0.098: 589 0.098 - 0.147: 129 0.147 - 0.196: 5 0.196 - 0.245: 3 Chirality restraints: 3240 Sorted by residual: chirality pdb=" CG LEU G 58 " pdb=" CB LEU G 58 " pdb=" CD1 LEU G 58 " pdb=" CD2 LEU G 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL L 16 " pdb=" N VAL L 16 " pdb=" C VAL L 16 " pdb=" CB VAL L 16 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3237 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 47 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL A 47 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL A 47 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR K 58 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO K 59 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 59 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 59 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " 0.014 2.00e-02 2.50e+03 1.39e-02 3.85e+00 pdb=" CG TYR H 80 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " 0.000 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2868 2.76 - 3.29: 19701 3.29 - 3.83: 37256 3.83 - 4.36: 40369 4.36 - 4.90: 61704 Nonbonded interactions: 161898 Sorted by model distance: nonbonded pdb=" O GLU K 91 " pdb=" ND2 ASN K 101 " model vdw 2.220 3.120 nonbonded pdb=" O ASP F 68 " pdb=" OG1 THR F 71 " model vdw 2.226 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.227 3.040 nonbonded pdb=" O ASN G 73 " pdb=" NZ LYS G 75 " model vdw 2.234 3.120 nonbonded pdb=" O2 DC I 19 " pdb=" N2 DG J 129 " model vdw 2.241 2.496 ... (remaining 161893 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 40 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 135)) selection = (chain 'E' and (resid 39 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 24 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 102)) selection = (chain 'F' and (resid 24 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 102)) } ncs_group { reference = (chain 'C' and (resid 13 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 94 or (r \ esid 95 and (name N or name CA or name C or name O or name CB )) or resid 96 thr \ ough 118)) selection = (chain 'G' and (resid 13 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 117 or (resid 118 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 30 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 74 or (resid 75 and (na \ me N or name CA or name C or name O or name CB )) or resid 76 through 121 or (re \ sid 122 and (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'H' and (resid 30 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 122)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.610 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19779 Z= 0.417 Angle : 0.719 10.154 27926 Z= 0.568 Chirality : 0.044 0.245 3240 Planarity : 0.004 0.051 2673 Dihedral : 25.934 176.591 7948 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.29 % Allowed : 34.17 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1754 helix: 1.30 (0.18), residues: 859 sheet: -0.15 (0.42), residues: 138 loop : -0.57 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.033 0.002 TYR H 80 PHE 0.012 0.001 PHE L 59 TRP 0.016 0.002 TRP L 276 HIS 0.004 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.42 (19779) covalent geometry : angle 0.71910 / 0.57 (27926) hydrogen bonds : bond 0.20999 / 14.33 ( 989) hydrogen bonds : angle 8.34944 / 6.00 ( 2630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.1187 time to fit residues: 14.0597 Evaluate side-chains 66 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain L residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 20.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN E 55 GLN ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 458 GLN K 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.068426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.040048 restraints weight = 133342.049| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 5.56 r_work: 0.2842 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19779 Z= 0.304 Angle : 0.749 9.277 27926 Z= 0.418 Chirality : 0.048 0.309 3240 Planarity : 0.005 0.056 2673 Dihedral : 28.433 176.111 4797 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.82 % Allowed : 30.72 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1754 helix: 1.35 (0.17), residues: 878 sheet: -0.07 (0.41), residues: 148 loop : -0.66 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 45 TYR 0.026 0.002 TYR H 80 PHE 0.015 0.001 PHE A 105 TRP 0.009 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.30 (19779) covalent geometry : angle 0.74943 / 0.42 (27926) hydrogen bonds : bond 0.09517 / 6.67 ( 989) hydrogen bonds : angle 5.33173 / 3.89 ( 2630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 67 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: C 58 LEU cc_start: 0.9781 (OUTLIER) cc_final: 0.9429 (mm) REVERT: C 65 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8880 (mm) REVERT: E 108 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9067 (p0) REVERT: F 35 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8537 (ttt90) REVERT: G 75 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9071 (mtmm) REVERT: G 83 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8953 (mp) outliers start: 67 outliers final: 24 residues processed: 132 average time/residue: 0.1299 time to fit residues: 27.6603 Evaluate side-chains 94 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 500 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 102 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 0.0270 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN E 108 ASN ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.069456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.040957 restraints weight = 129297.742| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.91 r_work: 0.2883 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19779 Z= 0.188 Angle : 0.651 8.860 27926 Z= 0.368 Chirality : 0.045 0.341 3240 Planarity : 0.004 0.052 2673 Dihedral : 28.453 179.642 4794 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.81 % Allowed : 30.00 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1754 helix: 1.52 (0.17), residues: 881 sheet: -0.23 (0.40), residues: 154 loop : -0.65 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 45 TYR 0.014 0.001 TYR H 37 PHE 0.013 0.001 PHE K 131 TRP 0.009 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (19779) covalent geometry : angle 0.65140 / 0.37 (27926) hydrogen bonds : bond 0.07611 / 5.26 ( 989) hydrogen bonds : angle 4.90997 / 3.59 ( 2630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 68 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: C 64 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8937 (tm-30) REVERT: E 108 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8969 (p0) REVERT: F 35 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8553 (ttt90) REVERT: G 75 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9126 (mtmm) REVERT: G 104 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8769 (tp40) outliers start: 53 outliers final: 24 residues processed: 119 average time/residue: 0.1258 time to fit residues: 24.5690 Evaluate side-chains 96 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 198 optimal weight: 30.0000 chunk 137 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** K 359 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 = 0.3973 r_free = 0.3973 target = 0.067564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.038552 restraints weight = 133486.432| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 5.97 r_work: 0.2780 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 19779 Z= 0.367 Angle : 0.774 9.013 27926 Z= 0.425 Chirality : 0.049 0.336 3240 Planarity : 0.005 0.053 2673 Dihedral : 28.582 178.793 4794 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.75 % Allowed : 30.50 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1754 helix: 1.24 (0.17), residues: 880 sheet: -0.32 (0.39), residues: 154 loop : -0.65 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 76 TYR 0.032 0.002 TYR L 74 PHE 0.017 0.002 PHE E 84 TRP 0.010 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.37 (19779) covalent geometry : angle 0.77443 / 0.43 (27926) hydrogen bonds : bond 0.08886 / 6.18 ( 989) hydrogen bonds : angle 5.21763 / 3.80 ( 2630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 67 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: C 23 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9132 (mm) REVERT: C 58 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9411 (mm) REVERT: C 64 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8946 (tm-30) REVERT: C 65 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8571 (mm) REVERT: D 122 LYS cc_start: 0.8955 (mttp) cc_final: 0.8722 (mmmt) REVERT: E 105 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9046 (mt-10) REVERT: F 35 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8602 (ttt90) REVERT: G 75 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9151 (mtmm) REVERT: L 476 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5327 (pp) outliers start: 66 outliers final: 39 residues processed: 130 average time/residue: 0.1245 time to fit residues: 26.5984 Evaluate side-chains 111 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 249 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 476 LEU Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 156 optimal weight: 6.9990 chunk 109 optimal weight: 0.0040 chunk 187 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 101 optimal weight: 0.0970 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 overall best weight: 2.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.068417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.039570 restraints weight = 131485.773| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 5.84 r_work: 0.2816 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19779 Z= 0.224 Angle : 0.671 7.911 27926 Z= 0.375 Chirality : 0.046 0.361 3240 Planarity : 0.004 0.051 2673 Dihedral : 28.561 179.474 4794 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.17 % Allowed : 31.29 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1754 helix: 1.43 (0.17), residues: 883 sheet: -0.33 (0.40), residues: 154 loop : -0.65 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 45 TYR 0.024 0.002 TYR L 74 PHE 0.016 0.001 PHE K 131 TRP 0.008 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (19779) covalent geometry : angle 0.67121 / 0.37 (27926) hydrogen bonds : bond 0.07329 / 5.07 ( 989) hydrogen bonds : angle 4.88394 / 3.58 ( 2630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 67 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 88 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: C 64 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8954 (tm-30) REVERT: C 65 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8524 (mm) REVERT: F 35 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8542 (ttt90) REVERT: G 75 LYS cc_start: 0.9530 (OUTLIER) cc_final: 0.9144 (mtmm) REVERT: K 400 TYR cc_start: 0.9324 (t80) cc_final: 0.8796 (t80) outliers start: 58 outliers final: 38 residues processed: 121 average time/residue: 0.1248 time to fit residues: 24.7927 Evaluate side-chains 107 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 515 MET Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.068407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.039603 restraints weight = 131323.604| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 5.88 r_work: 0.2822 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19779 Z= 0.193 Angle : 0.656 9.705 27926 Z= 0.364 Chirality : 0.045 0.358 3240 Planarity : 0.004 0.051 2673 Dihedral : 28.460 179.758 4794 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.24 % Allowed : 31.37 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1754 helix: 1.50 (0.17), residues: 883 sheet: -0.28 (0.40), residues: 154 loop : -0.68 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.023 0.002 TYR L 74 PHE 0.016 0.001 PHE K 131 TRP 0.009 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (19779) covalent geometry : angle 0.65581 / 0.36 (27926) hydrogen bonds : bond 0.06851 / 4.73 ( 989) hydrogen bonds : angle 4.74641 / 3.49 ( 2630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 66 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: B 88 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: C 23 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9009 (mm) REVERT: C 64 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8945 (tm-30) REVERT: C 65 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8561 (mm) REVERT: F 35 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8527 (ttt90) REVERT: F 45 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8362 (mtm180) REVERT: G 75 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9138 (mtmm) REVERT: K 400 TYR cc_start: 0.9317 (t80) cc_final: 0.8802 (t80) outliers start: 59 outliers final: 39 residues processed: 120 average time/residue: 0.1302 time to fit residues: 25.5742 Evaluate side-chains 110 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 249 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 515 MET Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 164 optimal weight: 50.0000 chunk 125 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.068823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040029 restraints weight = 131172.564| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 5.71 r_work: 0.2843 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19779 Z= 0.159 Angle : 0.630 10.735 27926 Z= 0.351 Chirality : 0.044 0.356 3240 Planarity : 0.004 0.050 2673 Dihedral : 28.371 179.933 4794 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.45 % Allowed : 32.37 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1754 helix: 1.65 (0.17), residues: 883 sheet: -0.23 (0.40), residues: 154 loop : -0.65 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.018 0.001 TYR L 74 PHE 0.017 0.001 PHE K 131 TRP 0.014 0.001 TRP L 276 HIS 0.004 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (19779) covalent geometry : angle 0.62952 / 0.35 (27926) hydrogen bonds : bond 0.06369 / 4.37 ( 989) hydrogen bonds : angle 4.57450 / 3.37 ( 2630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 72 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: B 88 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: C 23 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8977 (mm) REVERT: C 64 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8936 (tm-30) REVERT: C 65 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8547 (mm) REVERT: F 35 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8551 (ttt90) REVERT: F 45 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8317 (mtm180) REVERT: G 75 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.8961 (mtmm) REVERT: H 31 LYS cc_start: 0.9186 (mptt) cc_final: 0.8985 (mmtt) REVERT: K 400 TYR cc_start: 0.9292 (t80) cc_final: 0.8743 (t80) outliers start: 48 outliers final: 35 residues processed: 114 average time/residue: 0.1298 time to fit residues: 23.8543 Evaluate side-chains 107 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 65 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 249 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 515 MET Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 113 optimal weight: 0.0670 chunk 192 optimal weight: 10.0000 chunk 83 optimal weight: 0.0770 chunk 183 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 overall best weight: 2.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN ** K 359 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 = 0.3991 r_free = 0.3991 target = 0.068159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.039402 restraints weight = 131116.270| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 5.85 r_work: 0.2815 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19779 Z= 0.220 Angle : 0.667 10.606 27926 Z= 0.368 Chirality : 0.044 0.348 3240 Planarity : 0.004 0.052 2673 Dihedral : 28.418 179.936 4794 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.32 % Allowed : 31.29 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1754 helix: 1.53 (0.17), residues: 889 sheet: -0.42 (0.40), residues: 154 loop : -0.63 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.021 0.002 TYR L 74 PHE 0.017 0.001 PHE K 131 TRP 0.014 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (19779) covalent geometry : angle 0.66750 / 0.37 (27926) hydrogen bonds : bond 0.06780 / 4.67 ( 989) hydrogen bonds : angle 4.64969 / 3.42 ( 2630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 68 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 88 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: C 23 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9015 (mm) REVERT: C 64 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8930 (tm-30) REVERT: C 65 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8508 (mm) REVERT: F 35 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8543 (ttt90) REVERT: F 45 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8356 (mtm180) REVERT: G 75 LYS cc_start: 0.9519 (OUTLIER) cc_final: 0.9141 (mtmm) REVERT: K 400 TYR cc_start: 0.9262 (t80) cc_final: 0.8710 (t80) outliers start: 60 outliers final: 45 residues processed: 122 average time/residue: 0.1356 time to fit residues: 26.6941 Evaluate side-chains 117 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 65 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 488 ARG Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 249 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 515 MET Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 130 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.068796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040016 restraints weight = 130491.163| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 5.74 r_work: 0.2842 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19779 Z= 0.158 Angle : 0.638 12.017 27926 Z= 0.352 Chirality : 0.044 0.368 3240 Planarity : 0.004 0.050 2673 Dihedral : 28.390 179.489 4794 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.81 % Allowed : 32.01 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1754 helix: 1.56 (0.17), residues: 895 sheet: -0.40 (0.40), residues: 154 loop : -0.60 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 77 TYR 0.024 0.001 TYR L 74 PHE 0.017 0.001 PHE K 131 TRP 0.012 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (19779) covalent geometry : angle 0.63796 / 0.35 (27926) hydrogen bonds : bond 0.06248 / 4.28 ( 989) hydrogen bonds : angle 4.52310 / 3.34 ( 2630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 73 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: B 88 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: C 23 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.8972 (mm) REVERT: C 64 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8917 (tm-30) REVERT: C 65 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8536 (mm) REVERT: F 35 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8576 (ttt90) REVERT: F 45 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8313 (mtm180) REVERT: H 31 LYS cc_start: 0.9173 (mptt) cc_final: 0.8934 (mmtt) REVERT: K 400 TYR cc_start: 0.9229 (t80) cc_final: 0.8673 (t80) outliers start: 53 outliers final: 40 residues processed: 121 average time/residue: 0.1227 time to fit residues: 23.8438 Evaluate side-chains 114 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 68 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 488 ARG Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 249 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 515 MET Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 6 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 58 optimal weight: 0.0670 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.068777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040102 restraints weight = 130077.267| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 5.49 r_work: 0.2851 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19779 Z= 0.159 Angle : 0.644 11.671 27926 Z= 0.354 Chirality : 0.043 0.347 3240 Planarity : 0.004 0.054 2673 Dihedral : 28.368 179.962 4794 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.09 % Allowed : 32.37 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1754 helix: 1.59 (0.17), residues: 895 sheet: -0.42 (0.40), residues: 155 loop : -0.58 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.023 0.001 TYR L 74 PHE 0.020 0.001 PHE K 131 TRP 0.014 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (19779) covalent geometry : angle 0.64360 / 0.35 (27926) hydrogen bonds : bond 0.06201 / 4.25 ( 989) hydrogen bonds : angle 4.48369 / 3.32 ( 2630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 72 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: B 88 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: C 23 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8966 (mm) REVERT: C 64 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8923 (tm-30) REVERT: C 65 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8510 (mm) REVERT: F 35 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8575 (ttt90) REVERT: F 45 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8316 (mtm180) REVERT: H 31 LYS cc_start: 0.9099 (mptt) cc_final: 0.8851 (mmtt) REVERT: K 400 TYR cc_start: 0.9214 (t80) cc_final: 0.8645 (t80) outliers start: 43 outliers final: 35 residues processed: 109 average time/residue: 0.1271 time to fit residues: 22.5068 Evaluate side-chains 110 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 488 ARG Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 249 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 283 THR Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 339 CYS Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 447 THR Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 515 MET Chi-restraints excluded: chain L residue 516 LEU Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 74 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 0.0980 chunk 195 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.068206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.039456 restraints weight = 131088.051| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 5.68 r_work: 0.2825 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19779 Z= 0.207 Angle : 0.662 11.516 27926 Z= 0.363 Chirality : 0.044 0.345 3240 Planarity : 0.004 0.055 2673 Dihedral : 28.450 179.639 4794 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.31 % Allowed : 32.23 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1754 helix: 1.50 (0.17), residues: 896 sheet: -0.43 (0.40), residues: 155 loop : -0.58 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.026 0.002 TYR L 74 PHE 0.016 0.001 PHE K 131 TRP 0.015 0.002 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (19779) covalent geometry : angle 0.66167 / 0.36 (27926) hydrogen bonds : bond 0.06545 / 4.51 ( 989) hydrogen bonds : angle 4.57046 / 3.37 ( 2630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8236.18 seconds wall clock time: 140 minutes 36.39 seconds (8436.39 seconds total)