Starting phenix.real_space_refine on Thu Feb 5 17:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igw_52860/02_2026/9igw_52860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igw_52860/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9igw_52860/02_2026/9igw_52860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igw_52860/02_2026/9igw_52860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9igw_52860/02_2026/9igw_52860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igw_52860/02_2026/9igw_52860.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18912 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 634 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "K" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3641 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 218 Chain: "L" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3960 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 9, 'HIS:plan': 2, 'TYR:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 160 Chain: "I" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2687 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2725 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Time building chain proxies: 4.11, per 1000 atoms: 0.22 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: 1.71 Conformation dependent library (CDL) restraints added in 649.0 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: 2.67 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: 4.52 Time building geometry restraints manager: 2.21 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=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.43e+00 bond pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.67e+00 bond pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" N PHE H 67 " pdb=" CA PHE H 67 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.16e-02 7.43e+03 5.20e+00 bond pdb=" N GLU D 68 " pdb=" CA GLU D 68 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.16e+00 ... (remaining 19774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 27367 2.03 - 4.06: 503 4.06 - 6.09: 39 6.09 - 8.12: 14 8.12 - 10.15: 3 Bond angle restraints: 27926 Sorted by residual: 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 angle pdb=" N GLU A 51 " pdb=" CA GLU A 51 " pdb=" CB GLU A 51 " ideal model delta sigma weight residual 110.39 117.97 -7.58 1.66e+00 3.63e-01 2.09e+01 angle pdb=" CA GLU A 51 " pdb=" CB GLU A 51 " pdb=" CG GLU A 51 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" N ASN H 64 " pdb=" CA ASN H 64 " pdb=" C ASN H 64 " ideal model delta sigma weight residual 112.54 107.35 5.19 1.22e+00 6.72e-01 1.81e+01 angle pdb=" N ALA G 21 " pdb=" CA ALA G 21 " pdb=" C ALA G 21 " ideal model delta sigma weight residual 114.75 109.39 5.36 1.26e+00 6.30e-01 1.81e+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: 2744 0.049 - 0.098: 404 0.098 - 0.147: 86 0.147 - 0.196: 3 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: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 0.004 0.040 19779 Z= 0.184 Angle : 0.616 10.154 27926 Z= 0.360 Chirality : 0.037 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 covalent geometry : bond 0.00379 (19779) covalent geometry : angle 0.61583 (27926) hydrogen bonds : bond 0.20999 ( 989) hydrogen bonds : angle 8.34944 ( 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 : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.1231 time to fit residues: 14.1779 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 : 0.473 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3995 r_free = 0.3995 target = 0.068248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.039540 restraints weight = 132242.370| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 5.84 r_work: 0.2826 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19779 Z= 0.327 Angle : 0.663 7.815 27926 Z= 0.379 Chirality : 0.042 0.173 3240 Planarity : 0.005 0.054 2673 Dihedral : 28.288 179.166 4797 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.60 % Allowed : 30.07 % Favored : 65.32 % 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: 0.62 (0.20), residues: 1754 helix: 1.39 (0.17), residues: 879 sheet: -0.21 (0.41), residues: 154 loop : -0.61 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.022 0.002 TYR H 80 PHE 0.014 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 covalent geometry : bond 0.00725 (19779) covalent geometry : angle 0.66306 (27926) hydrogen bonds : bond 0.08077 ( 989) hydrogen bonds : angle 5.12656 ( 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 132 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 68 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8883 (mm) REVERT: E 108 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9134 (p0) REVERT: F 35 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8591 (ttt90) REVERT: G 75 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9111 (mtmm) REVERT: G 83 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8947 (mp) REVERT: K 135 MET cc_start: 0.5267 (ppp) cc_final: 0.5042 (ppp) outliers start: 64 outliers final: 23 residues processed: 129 average time/residue: 0.1222 time to fit residues: 25.1325 Evaluate side-chains 90 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 68 ASN 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 84 SER Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 16 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 339 CYS Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 528 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 102 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN E 108 ASN 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 = 0.4016 r_free = 0.4016 target = 0.069088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.040704 restraints weight = 131943.406| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 6.01 r_work: 0.2864 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19779 Z= 0.187 Angle : 0.588 8.315 27926 Z= 0.333 Chirality : 0.038 0.150 3240 Planarity : 0.004 0.052 2673 Dihedral : 28.159 179.885 4794 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.74 % Allowed : 30.36 % Favored : 65.90 % 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: 0.79 (0.20), residues: 1754 helix: 1.62 (0.17), residues: 883 sheet: -0.28 (0.40), residues: 154 loop : -0.64 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 84 TYR 0.017 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 covalent geometry : bond 0.00414 (19779) covalent geometry : angle 0.58841 (27926) hydrogen bonds : bond 0.06470 ( 989) hydrogen bonds : angle 4.71409 ( 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 125 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 73 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8817 (tp) REVERT: B 88 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 58 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9408 (mm) REVERT: C 64 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8958 (tm-30) REVERT: C 65 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8596 (mm) REVERT: D 56 MET cc_start: 0.9137 (tpp) cc_final: 0.8933 (tpp) REVERT: E 108 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.9005 (p0) REVERT: F 35 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8569 (ttt90) outliers start: 52 outliers final: 22 residues processed: 122 average time/residue: 0.1146 time to fit residues: 22.8572 Evaluate side-chains 95 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 62 LEU 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 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 50 GLU 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 58 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 H residue 29 SER Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 ASP 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 500 HIS Chi-restraints excluded: chain L residue 512 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 91 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 137 optimal weight: 0.0470 chunk 151 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** F 75 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 = 0.4033 r_free = 0.4033 target = 0.069362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.041101 restraints weight = 129844.928| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 5.81 r_work: 0.2895 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19779 Z= 0.166 Angle : 0.573 7.774 27926 Z= 0.325 Chirality : 0.037 0.153 3240 Planarity : 0.004 0.056 2673 Dihedral : 28.011 179.449 4794 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.31 % Allowed : 30.29 % Favored : 66.40 % 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: 0.89 (0.20), residues: 1754 helix: 1.72 (0.17), residues: 883 sheet: -0.24 (0.40), residues: 154 loop : -0.62 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.015 0.001 TYR H 37 PHE 0.017 0.001 PHE K 131 TRP 0.011 0.001 TRP L 276 HIS 0.004 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00366 (19779) covalent geometry : angle 0.57350 (27926) hydrogen bonds : bond 0.06019 ( 989) hydrogen bonds : angle 4.52078 ( 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 120 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 74 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8803 (tp) REVERT: B 88 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: C 58 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9399 (mm) REVERT: C 64 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8958 (tm-30) REVERT: C 65 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8557 (mm) REVERT: F 35 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8617 (ttt90) REVERT: F 59 LYS cc_start: 0.9523 (tppt) cc_final: 0.9145 (tppt) REVERT: K 400 TYR cc_start: 0.9260 (t80) cc_final: 0.8692 (t80) outliers start: 46 outliers final: 26 residues processed: 115 average time/residue: 0.1201 time to fit residues: 22.5310 Evaluate side-chains 99 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 62 LEU 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 16 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 LEU 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 H residue 29 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain L residue 16 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 156 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 0.0170 chunk 101 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 198 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 overall best weight: 2.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.068452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.039640 restraints weight = 131666.823| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 5.84 r_work: 0.2828 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19779 Z= 0.252 Angle : 0.598 8.554 27926 Z= 0.340 Chirality : 0.039 0.141 3240 Planarity : 0.004 0.053 2673 Dihedral : 28.091 179.963 4794 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.24 % Allowed : 29.50 % Favored : 66.26 % 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: 1.64 (0.17), residues: 885 sheet: -0.29 (0.39), residues: 159 loop : -0.59 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.017 0.002 TYR G 57 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 covalent geometry : bond 0.00561 (19779) covalent geometry : angle 0.59829 (27926) hydrogen bonds : bond 0.06428 ( 989) hydrogen bonds : angle 4.64247 ( 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 129 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 70 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: B 88 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: C 23 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9033 (mm) REVERT: C 58 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9383 (mm) REVERT: C 64 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8931 (tm-30) REVERT: C 65 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8568 (mm) REVERT: E 108 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.9048 (p0) REVERT: F 35 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8553 (ttt90) REVERT: G 77 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7210 (mmt90) REVERT: G 104 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8779 (tp40) REVERT: K 400 TYR cc_start: 0.9251 (t80) cc_final: 0.8704 (t80) outliers start: 59 outliers final: 37 residues processed: 125 average time/residue: 0.1156 time to fit residues: 23.7298 Evaluate side-chains 111 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 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 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 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 16 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain K residue 286 ILE Chi-restraints excluded: chain L residue 16 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** F 75 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 = 0.4008 r_free = 0.4008 target = 0.068955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.040225 restraints weight = 130060.578| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 5.83 r_work: 0.2846 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19779 Z= 0.188 Angle : 0.578 9.730 27926 Z= 0.325 Chirality : 0.037 0.144 3240 Planarity : 0.004 0.055 2673 Dihedral : 28.074 179.810 4794 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.74 % Allowed : 30.79 % Favored : 65.47 % 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: 0.88 (0.20), residues: 1754 helix: 1.68 (0.17), residues: 891 sheet: -0.36 (0.40), residues: 155 loop : -0.57 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.014 0.001 TYR G 57 PHE 0.018 0.001 PHE K 131 TRP 0.012 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00417 (19779) covalent geometry : angle 0.57768 (27926) hydrogen bonds : bond 0.05864 ( 989) hydrogen bonds : angle 4.47149 ( 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 124 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 72 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 88 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: C 23 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8985 (mm) REVERT: C 58 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9396 (mm) REVERT: C 64 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8948 (tm-30) REVERT: C 65 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8549 (mm) REVERT: E 108 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.9066 (p0) REVERT: F 35 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8630 (ttt90) REVERT: H 31 LYS cc_start: 0.9175 (mmtm) cc_final: 0.8885 (mmtt) REVERT: K 400 TYR cc_start: 0.9202 (t80) cc_final: 0.8652 (t80) outliers start: 52 outliers final: 36 residues processed: 120 average time/residue: 0.1174 time to fit residues: 22.4330 Evaluate side-chains 110 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 65 LEU 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 108 ASN 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 76 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 286 ILE Chi-restraints excluded: chain K residue 488 ARG Chi-restraints excluded: chain L residue 16 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 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 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: 3.9990 chunk 5 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 61 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 chunk 32 optimal weight: 0.2980 chunk 164 optimal weight: 40.0000 chunk 125 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** F 75 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 = 0.4019 r_free = 0.4019 target = 0.069334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.040701 restraints weight = 130062.348| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 5.75 r_work: 0.2872 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19779 Z= 0.156 Angle : 0.571 11.330 27926 Z= 0.319 Chirality : 0.037 0.256 3240 Planarity : 0.004 0.052 2673 Dihedral : 27.978 179.821 4794 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.31 % Allowed : 30.79 % Favored : 65.90 % 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: 0.93 (0.20), residues: 1754 helix: 1.73 (0.17), residues: 891 sheet: -0.29 (0.41), residues: 148 loop : -0.57 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.014 0.001 TYR H 37 PHE 0.017 0.001 PHE K 131 TRP 0.011 0.001 TRP L 276 HIS 0.004 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00343 (19779) covalent geometry : angle 0.57069 (27926) hydrogen bonds : bond 0.05622 ( 989) hydrogen bonds : angle 4.32607 ( 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 119 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 73 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 88 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: C 23 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8962 (mm) REVERT: C 58 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9357 (mm) REVERT: C 64 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8939 (tm-30) REVERT: C 65 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8561 (mm) REVERT: D 56 MET cc_start: 0.9147 (tpp) cc_final: 0.8924 (tpp) REVERT: F 35 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8640 (ttt90) REVERT: G 71 ARG cc_start: 0.9019 (ttp80) cc_final: 0.8724 (ttp80) REVERT: H 31 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8884 (mmtt) REVERT: K 400 TYR cc_start: 0.9162 (t80) cc_final: 0.8587 (t80) outliers start: 46 outliers final: 30 residues processed: 115 average time/residue: 0.1202 time to fit residues: 22.4128 Evaluate side-chains 105 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 88 TYR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 286 ILE Chi-restraints excluded: chain K residue 488 ARG 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 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 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: 10.0000 chunk 192 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN K 152 ASN ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.067321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.038412 restraints weight = 132808.721| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 5.89 r_work: 0.2782 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 19779 Z= 0.367 Angle : 0.674 10.334 27926 Z= 0.377 Chirality : 0.042 0.164 3240 Planarity : 0.004 0.052 2673 Dihedral : 28.298 179.338 4794 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.46 % Allowed : 30.07 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1754 helix: 1.41 (0.17), residues: 895 sheet: -0.35 (0.41), residues: 148 loop : -0.55 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 84 TYR 0.021 0.002 TYR G 57 PHE 0.017 0.001 PHE K 131 TRP 0.011 0.002 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00818 (19779) covalent geometry : angle 0.67370 (27926) hydrogen bonds : bond 0.07295 ( 989) hydrogen bonds : angle 4.78676 ( 2630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 66 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: C 23 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9067 (mm) REVERT: C 58 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9411 (mm) REVERT: C 64 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8964 (tm-30) REVERT: C 65 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8616 (mm) REVERT: F 35 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8639 (ttt90) REVERT: F 45 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8790 (mtp180) REVERT: K 400 TYR cc_start: 0.9210 (t80) cc_final: 0.8653 (t80) outliers start: 62 outliers final: 39 residues processed: 125 average time/residue: 0.1159 time to fit residues: 23.0907 Evaluate side-chains 108 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 63 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 109 ASN 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 58 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 82 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 286 ILE 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 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 246 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 130 optimal weight: 30.0000 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 129 optimal weight: 0.0470 chunk 100 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** F 75 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 = 0.4015 r_free = 0.4015 target = 0.069202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.040575 restraints weight = 129742.415| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 5.71 r_work: 0.2864 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19779 Z= 0.148 Angle : 0.602 11.409 27926 Z= 0.332 Chirality : 0.037 0.134 3240 Planarity : 0.004 0.054 2673 Dihedral : 28.206 179.155 4794 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.88 % Allowed : 31.44 % Favored : 65.68 % 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: 0.81 (0.20), residues: 1754 helix: 1.57 (0.17), residues: 895 sheet: -0.34 (0.41), residues: 150 loop : -0.55 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 232 TYR 0.014 0.001 TYR H 37 PHE 0.019 0.001 PHE K 131 TRP 0.010 0.002 TRP L 276 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00323 (19779) covalent geometry : angle 0.60182 (27926) hydrogen bonds : bond 0.05713 ( 989) hydrogen bonds : angle 4.38808 ( 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 114 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: C 23 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8944 (mm) REVERT: C 64 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8942 (tm-30) REVERT: C 65 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8521 (mm) REVERT: F 45 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8247 (mtm180) REVERT: K 400 TYR cc_start: 0.9135 (t80) cc_final: 0.8562 (t80) outliers start: 40 outliers final: 32 residues processed: 110 average time/residue: 0.1243 time to fit residues: 21.6387 Evaluate side-chains 105 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 109 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 47 SER 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 E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 84 SER 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 97 LYS 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 246 HIS 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 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 6 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 172 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 118 optimal weight: 30.0000 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 137 optimal weight: 50.0000 chunk 58 optimal weight: 0.7980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.068686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.040466 restraints weight = 129956.753| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 5.45 r_work: 0.2849 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19779 Z= 0.185 Angle : 0.599 11.544 27926 Z= 0.332 Chirality : 0.037 0.134 3240 Planarity : 0.004 0.054 2673 Dihedral : 28.137 179.861 4794 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.95 % Allowed : 30.94 % 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: 0.85 (0.20), residues: 1754 helix: 1.61 (0.17), residues: 895 sheet: -0.27 (0.42), residues: 138 loop : -0.57 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 232 TYR 0.017 0.001 TYR D 118 PHE 0.016 0.001 PHE K 131 TRP 0.008 0.001 TRP L 276 HIS 0.004 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00414 (19779) covalent geometry : angle 0.59932 (27926) hydrogen bonds : bond 0.05835 ( 989) hydrogen bonds : angle 4.38148 ( 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 110 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: B 88 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: C 23 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8973 (mm) REVERT: C 64 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8936 (tm-30) REVERT: C 65 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8538 (mm) REVERT: K 48 MET cc_start: 0.3066 (ptt) cc_final: 0.2754 (mtm) REVERT: K 400 TYR cc_start: 0.9155 (t80) cc_final: 0.8588 (t80) REVERT: L 461 MET cc_start: 0.4028 (mmt) cc_final: 0.3723 (mmt) outliers start: 41 outliers final: 33 residues processed: 106 average time/residue: 0.1133 time to fit residues: 19.8538 Evaluate side-chains 105 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 C residue 65 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 84 SER 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 97 LYS 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 246 HIS 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 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 74 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 40.0000 chunk 153 optimal weight: 0.0270 chunk 109 optimal weight: 20.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3997 r_free = 0.3997 target = 0.071142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.043978 restraints weight = 145055.197| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 5.95 r_work: 0.2798 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 19779 Z= 0.305 Angle : 0.659 11.714 27926 Z= 0.366 Chirality : 0.040 0.158 3240 Planarity : 0.004 0.054 2673 Dihedral : 28.371 179.504 4794 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.73 % Allowed : 31.22 % Favored : 66.04 % 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: 0.64 (0.20), residues: 1754 helix: 1.41 (0.17), residues: 895 sheet: -0.35 (0.41), residues: 138 loop : -0.61 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 232 TYR 0.020 0.002 TYR D 118 PHE 0.018 0.001 PHE K 131 TRP 0.012 0.001 TRP L 276 HIS 0.005 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00680 (19779) covalent geometry : angle 0.65913 (27926) hydrogen bonds : bond 0.06837 ( 989) hydrogen bonds : angle 4.65195 ( 2630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8008.79 seconds wall clock time: 136 minutes 38.12 seconds (8198.12 seconds total)