Starting phenix.real_space_refine on Sat Jul 4 07:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igw_52860/07_2026/9igw_52860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igw_52860/07_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_52860/07_2026/9igw_52860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igw_52860/07_2026/9igw_52860.map" model { file = "/net/cci-nas-00/data/ceres_data/9igw_52860/07_2026/9igw_52860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igw_52860/07_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-dev-6108/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: 3.79, per 1000 atoms: 0.20 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: 1.67 Conformation dependent library (CDL) restraints added in 668.3 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: 2.41 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: 3.82 Time building geometry restraints manager: 2.23 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: 27078 2.03 - 4.06: 791 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: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.460 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- 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 : 0.715 10.154 27926 Z= 0.564 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 0.71499 / 0.56 (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 : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.1170 time to fit residues: 13.9635 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 : 0.478 ------------------------------------------------------------------------------- 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: 9.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.068398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.039586 restraints weight = 133341.847| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 6.03 r_work: 0.2841 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19779 Z= 0.302 Angle : 0.746 9.322 27926 Z= 0.417 Chirality : 0.048 0.297 3240 Planarity : 0.005 0.055 2673 Dihedral : 28.494 176.244 4797 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.82 % Allowed : 30.50 % Favored : 64.68 % 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: 876 sheet: -0.08 (0.41), residues: 148 loop : -0.66 (0.24), residues: 730 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 0.008 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 0.74608 / 0.42 (27926) hydrogen bonds : bond 0.09434 / 6.61 ( 989) hydrogen bonds : angle 5.31869 / 3.88 ( 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 : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: C 58 LEU cc_start: 0.9781 (OUTLIER) cc_final: 0.9429 (mm) REVERT: C 65 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8889 (mm) REVERT: E 108 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9061 (p0) REVERT: F 35 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8549 (ttt90) REVERT: G 75 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9074 (mtmm) REVERT: G 83 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8969 (mp) outliers start: 67 outliers final: 24 residues processed: 132 average time/residue: 0.1242 time to fit residues: 26.3531 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 : 0.585 ------------------------------------------------------------------------------- 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: 0.4980 chunk 113 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 119 optimal weight: 0.0060 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- 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** K 458 GLN L 152 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.069416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.040901 restraints weight = 131412.276| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 5.90 r_work: 0.2885 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19779 Z= 0.174 Angle : 0.636 9.469 27926 Z= 0.363 Chirality : 0.045 0.320 3240 Planarity : 0.004 0.053 2673 Dihedral : 28.502 179.317 4794 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.60 % Allowed : 30.29 % Favored : 66.12 % 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: 0.73 (0.20), residues: 1754 helix: 1.54 (0.17), residues: 881 sheet: -0.22 (0.40), residues: 154 loop : -0.65 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.014 0.001 TYR H 37 PHE 0.014 0.001 PHE K 131 TRP 0.011 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (19779) covalent geometry : angle 0.63561 / 0.36 (27926) hydrogen bonds : bond 0.07620 / 5.26 ( 989) hydrogen bonds : angle 4.89290 / 3.58 ( 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 119 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 69 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: E 108 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8994 (p0) REVERT: F 35 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8521 (ttt90) REVERT: G 75 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9125 (mtmm) REVERT: G 104 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8774 (tp40) outliers start: 50 outliers final: 23 residues processed: 117 average time/residue: 0.1210 time to fit residues: 23.3076 Evaluate side-chains 96 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 528 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 50.0000 chunk 185 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN B 75 HIS E 108 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.068647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040004 restraints weight = 132038.191| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 5.91 r_work: 0.2841 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19779 Z= 0.222 Angle : 0.654 7.806 27926 Z= 0.370 Chirality : 0.044 0.316 3240 Planarity : 0.004 0.052 2673 Dihedral : 28.480 179.494 4794 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.10 % Allowed : 30.14 % Favored : 65.76 % 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: 0.73 (0.20), residues: 1754 helix: 1.55 (0.17), residues: 883 sheet: -0.27 (0.39), residues: 154 loop : -0.64 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.017 0.002 TYR A 42 PHE 0.015 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 0.00446 / 0.22 (19779) covalent geometry : angle 0.65434 / 0.37 (27926) hydrogen bonds : bond 0.07574 / 5.25 ( 989) hydrogen bonds : angle 4.85825 / 3.55 ( 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 126 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 69 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8820 (tp) REVERT: B 88 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: C 23 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9096 (mm) REVERT: C 65 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8878 (mm) REVERT: E 105 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8990 (mt-10) REVERT: F 35 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8561 (ttt90) REVERT: G 75 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9147 (mtmm) REVERT: G 104 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8793 (tp40) REVERT: K 400 TYR cc_start: 0.9318 (t80) cc_final: 0.8781 (t80) REVERT: L 476 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5258 (pp) outliers start: 57 outliers final: 34 residues processed: 122 average time/residue: 0.1226 time to fit residues: 24.5097 Evaluate side-chains 109 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 67 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU 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 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 58 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 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 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 113 VAL 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 476 LEU 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 528 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 156 optimal weight: 10.0000 chunk 109 optimal weight: 0.0670 chunk 187 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 chunk 101 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 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 = 0.3977 r_free = 0.3977 target = 0.067791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.038843 restraints weight = 133348.078| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 5.89 r_work: 0.2786 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 19779 Z= 0.329 Angle : 0.725 8.238 27926 Z= 0.403 Chirality : 0.047 0.325 3240 Planarity : 0.005 0.052 2673 Dihedral : 28.628 179.749 4794 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.32 % Allowed : 30.14 % 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: 0.56 (0.20), residues: 1754 helix: 1.34 (0.17), residues: 881 sheet: -0.32 (0.39), residues: 154 loop : -0.64 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 84 TYR 0.025 0.002 TYR A 42 PHE 0.015 0.002 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 0.00676 / 0.33 (19779) covalent geometry : angle 0.72499 / 0.40 (27926) hydrogen bonds : bond 0.08205 / 5.70 ( 989) hydrogen bonds : angle 5.05783 / 3.69 ( 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 142 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 68 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: C 23 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9144 (mm) REVERT: C 58 LEU cc_start: 0.9779 (OUTLIER) cc_final: 0.9395 (mm) REVERT: C 64 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8990 (tm-30) REVERT: C 65 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8624 (mm) REVERT: D 122 LYS cc_start: 0.8951 (mttp) cc_final: 0.8714 (mmmt) REVERT: F 35 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8588 (ttt90) REVERT: G 75 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9156 (mtmm) outliers start: 74 outliers final: 46 residues processed: 136 average time/residue: 0.1270 time to fit residues: 27.7268 Evaluate side-chains 118 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 66 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU 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 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 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 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 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 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 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: 10.0000 chunk 42 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 31 optimal weight: 0.6980 chunk 129 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.068410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.039484 restraints weight = 130714.000| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 5.83 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: 0.8789 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19779 Z= 0.222 Angle : 0.667 9.491 27926 Z= 0.372 Chirality : 0.045 0.339 3240 Planarity : 0.004 0.052 2673 Dihedral : 28.605 178.656 4794 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.53 % Allowed : 30.94 % 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: 1.44 (0.17), residues: 884 sheet: -0.32 (0.40), residues: 154 loop : -0.66 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.020 0.002 TYR G 57 PHE 0.017 0.001 PHE K 131 TRP 0.007 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (19779) covalent geometry : angle 0.66691 / 0.37 (27926) hydrogen bonds : bond 0.07176 / 4.96 ( 989) hydrogen bonds : angle 4.83932 / 3.55 ( 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 129 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 66 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: B 88 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: C 64 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8949 (tm-30) REVERT: C 65 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8578 (mm) REVERT: F 35 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8555 (ttt90) REVERT: G 75 LYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9158 (mtmm) REVERT: K 400 TYR cc_start: 0.9349 (t80) cc_final: 0.8821 (t80) outliers start: 63 outliers final: 45 residues processed: 125 average time/residue: 0.1103 time to fit residues: 22.8179 Evaluate side-chains 114 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 64 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 51 GLU 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 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 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 37 LEU 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 75 LYS Chi-restraints excluded: chain G residue 76 THR 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 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 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: 1.9990 chunk 5 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 164 optimal weight: 50.0000 chunk 125 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.069109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.040321 restraints weight = 130996.845| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 5.75 r_work: 0.2850 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19779 Z= 0.144 Angle : 0.625 11.525 27926 Z= 0.350 Chirality : 0.043 0.337 3240 Planarity : 0.004 0.050 2673 Dihedral : 28.427 178.858 4794 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.45 % Allowed : 32.52 % Favored : 64.03 % 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: 0.78 (0.20), residues: 1754 helix: 1.61 (0.17), residues: 884 sheet: -0.26 (0.40), residues: 154 loop : -0.66 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.019 0.002 TYR D 118 PHE 0.017 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 0.00266 / 0.14 (19779) covalent geometry : angle 0.62504 / 0.35 (27926) hydrogen bonds : bond 0.06321 / 4.32 ( 989) hydrogen bonds : angle 4.56651 / 3.36 ( 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 121 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 73 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8539 (tp) REVERT: A 134 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: B 88 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: C 23 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8974 (mm) REVERT: C 64 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8957 (tm-30) REVERT: F 35 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8587 (ttt90) REVERT: H 31 LYS cc_start: 0.9197 (mmtm) cc_final: 0.8916 (mmtt) REVERT: K 400 TYR cc_start: 0.9301 (t80) cc_final: 0.8770 (t80) outliers start: 48 outliers final: 30 residues processed: 114 average time/residue: 0.1290 time to fit residues: 23.6567 Evaluate side-chains 102 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 61 LEU 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 88 TYR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU 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 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 65 ASP 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: 0.0470 chunk 192 optimal weight: 10.0000 chunk 83 optimal weight: 0.0980 chunk 183 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 135 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 overall best weight: 3.2284 ------------------------------------------------------------------------------- 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 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 = 0.3987 r_free = 0.3987 target = 0.068069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.039227 restraints weight = 132042.619| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 5.85 r_work: 0.2805 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19779 Z= 0.246 Angle : 0.676 10.292 27926 Z= 0.374 Chirality : 0.044 0.325 3240 Planarity : 0.004 0.053 2673 Dihedral : 28.503 179.696 4794 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.53 % Allowed : 31.80 % Favored : 64.68 % 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: 0.70 (0.20), residues: 1754 helix: 1.50 (0.17), residues: 891 sheet: -0.43 (0.40), residues: 154 loop : -0.63 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.016 0.002 TYR G 57 PHE 0.017 0.001 PHE K 131 TRP 0.013 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.25 (19779) covalent geometry : angle 0.67569 / 0.37 (27926) hydrogen bonds : bond 0.06955 / 4.80 ( 989) hydrogen bonds : angle 4.73986 / 3.47 ( 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 119 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 70 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 23 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9020 (mm) REVERT: C 64 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8957 (tm-30) REVERT: C 65 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8561 (mm) REVERT: F 35 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8573 (ttt90) REVERT: F 45 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8350 (mtm180) REVERT: K 400 TYR cc_start: 0.9295 (t80) cc_final: 0.8777 (t80) outliers start: 49 outliers final: 36 residues processed: 113 average time/residue: 0.1206 time to fit residues: 22.0310 Evaluate side-chains 106 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 47 SER 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 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 120 MET 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 73 THR Chi-restraints excluded: chain F residue 82 THR 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 K residue 201 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 130 optimal weight: 8.9990 chunk 69 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 153 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 129 optimal weight: 30.0000 chunk 100 optimal weight: 0.0370 chunk 159 optimal weight: 0.0770 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.069408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.041212 restraints weight = 130448.621| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 5.54 r_work: 0.2864 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19779 Z= 0.135 Angle : 0.633 11.187 27926 Z= 0.352 Chirality : 0.043 0.335 3240 Planarity : 0.004 0.051 2673 Dihedral : 28.397 178.607 4794 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.30 % Allowed : 32.95 % 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: 0.80 (0.20), residues: 1754 helix: 1.61 (0.17), residues: 884 sheet: -0.27 (0.40), residues: 159 loop : -0.63 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.015 0.001 TYR H 37 PHE 0.018 0.001 PHE K 131 TRP 0.009 0.001 TRP L 276 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (19779) covalent geometry : angle 0.63291 / 0.35 (27926) hydrogen bonds : bond 0.06114 / 4.17 ( 989) hydrogen bonds : angle 4.44745 / 3.28 ( 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 108 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 64 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8940 (tm-30) REVERT: F 35 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8522 (ttt90) REVERT: K 400 TYR cc_start: 0.9255 (t80) cc_final: 0.8687 (t80) outliers start: 32 outliers final: 24 residues processed: 103 average time/residue: 0.1321 time to fit residues: 22.0133 Evaluate side-chains 97 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 51 LEU 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 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain K residue 201 ASP 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 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: 0.8980 chunk 196 optimal weight: 10.0000 chunk 172 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 108 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** 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 = 0.4007 r_free = 0.4007 target = 0.068856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.040194 restraints weight = 130615.562| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 5.77 r_work: 0.2844 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19779 Z= 0.162 Angle : 0.627 11.473 27926 Z= 0.349 Chirality : 0.043 0.322 3240 Planarity : 0.004 0.056 2673 Dihedral : 28.412 179.696 4794 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.23 % Allowed : 33.02 % 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: 0.84 (0.20), residues: 1754 helix: 1.65 (0.17), residues: 884 sheet: -0.25 (0.41), residues: 152 loop : -0.61 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.014 0.001 TYR H 37 PHE 0.019 0.001 PHE K 131 TRP 0.007 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (19779) covalent geometry : angle 0.62740 / 0.35 (27926) hydrogen bonds : bond 0.06194 / 4.24 ( 989) hydrogen bonds : angle 4.46039 / 3.28 ( 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 101 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: C 23 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.8981 (mm) REVERT: C 58 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9404 (mm) REVERT: C 64 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8957 (tm-30) REVERT: F 35 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8658 (ttt90) REVERT: K 400 TYR cc_start: 0.9280 (t80) cc_final: 0.8724 (t80) outliers start: 31 outliers final: 25 residues processed: 95 average time/residue: 0.1320 time to fit residues: 20.4868 Evaluate side-chains 98 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 134 GLU 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 E residue 50 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR 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 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 74 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 153 optimal weight: 0.0050 chunk 109 optimal weight: 7.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.068968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.040430 restraints weight = 130805.923| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.87 r_work: 0.2854 rms_B_bonded: 5.65 restraints_weight: 2.0000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19779 Z= 0.151 Angle : 0.622 11.599 27926 Z= 0.347 Chirality : 0.042 0.322 3240 Planarity : 0.004 0.057 2673 Dihedral : 28.402 179.102 4794 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.52 % Allowed : 32.81 % Favored : 64.68 % Cbeta Deviations : 0.06 % 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: 0.87 (0.20), residues: 1754 helix: 1.69 (0.17), residues: 884 sheet: -0.24 (0.40), residues: 159 loop : -0.61 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.014 0.001 TYR H 37 PHE 0.017 0.001 PHE K 131 TRP 0.013 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (19779) covalent geometry : angle 0.62195 / 0.35 (27926) hydrogen bonds : bond 0.06015 / 4.11 ( 989) hydrogen bonds : angle 4.39941 / 3.24 ( 2630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7800.51 seconds wall clock time: 133 minutes 21.81 seconds (8001.81 seconds total)