Starting phenix.real_space_refine on Fri Nov 21 00:21:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4x_48914/11_2025/9n4x_48914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4x_48914/11_2025/9n4x_48914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4x_48914/11_2025/9n4x_48914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4x_48914/11_2025/9n4x_48914.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4x_48914/11_2025/9n4x_48914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4x_48914/11_2025/9n4x_48914.cif" } resolution = 3.2 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 199 5.16 5 C 25372 2.51 5 N 6661 2.21 5 O 7618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39850 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3386 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 408} Chain breaks: 3 Chain: "B" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3402 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 409} Chain breaks: 5 Chain: "C" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3266 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 392} Chain breaks: 7 Chain: "D" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3176 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 379} Chain breaks: 9 Chain: "F" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3381 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 406} Chain breaks: 7 Chain: "E" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3263 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 24, 'TRANS': 388} Chain breaks: 6 Chain: "G" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3305 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 397} Chain breaks: 7 Chain: "H" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3132 Classifications: {'peptide': 397} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 377} Chain breaks: 7 Chain: "I" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3336 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 402} Chain breaks: 5 Chain: "J" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3368 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 407} Chain breaks: 6 Chain: "L" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3408 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 3 Chain: "K" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3427 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 3 Time building chain proxies: 9.83, per 1000 atoms: 0.25 Number of scatterers: 39850 At special positions: 0 Unit cell: (122.2, 150.15, 158.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 199 16.00 O 7618 8.00 N 6661 7.00 C 25372 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: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9366 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 43 sheets defined 42.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.758A pdb=" N GLY A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 227 through 248 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 303 through 312 removed outlier: 4.045A pdb=" N GLY A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.503A pdb=" N ARG A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 434 through 454 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.701A pdb=" N TYR A 461 " --> pdb=" O HIS A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.662A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 227 through 248 Processing helix chain 'B' and resid 290 through 303 Processing helix chain 'B' and resid 303 through 312 removed outlier: 4.039A pdb=" N GLY B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 321 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.511A pdb=" N ARG B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 434 through 454 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 102 through 118 removed outlier: 4.088A pdb=" N GLY C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 227 through 248 Processing helix chain 'C' and resid 291 through 303 Processing helix chain 'C' and resid 303 through 312 removed outlier: 3.920A pdb=" N GLY C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 365 through 384 Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 434 through 454 Processing helix chain 'C' and resid 457 through 464 Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.501A pdb=" N ALA D 73 " --> pdb=" O ASP D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 156 through 161 removed outlier: 3.680A pdb=" N THR D 159 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP D 160 " --> pdb=" O TRP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 226 through 248 Processing helix chain 'D' and resid 291 through 303 removed outlier: 3.579A pdb=" N TYR D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.706A pdb=" N GLY D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 365 through 383 Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 455 removed outlier: 3.924A pdb=" N PHE D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 removed outlier: 3.608A pdb=" N TYR D 461 " --> pdb=" O HIS D 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 102 through 118 removed outlier: 3.712A pdb=" N GLY F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 227 through 248 Processing helix chain 'F' and resid 290 through 303 Processing helix chain 'F' and resid 303 through 312 removed outlier: 4.236A pdb=" N GLY F 309 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 3.954A pdb=" N TYR F 318 " --> pdb=" O SER F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 384 Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 434 through 454 Processing helix chain 'F' and resid 457 through 465 removed outlier: 3.506A pdb=" N TYR F 461 " --> pdb=" O HIS F 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.808A pdb=" N SER E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR E 117 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 226 through 248 Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 303 through 312 removed outlier: 4.087A pdb=" N GLY E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 319 removed outlier: 3.801A pdb=" N TYR E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 384 Processing helix chain 'E' and resid 412 through 422 Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 430 through 432 No H-bonds generated for 'chain 'E' and resid 430 through 432' Processing helix chain 'E' and resid 434 through 454 Processing helix chain 'E' and resid 457 through 464 Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.950A pdb=" N SER G 52 " --> pdb=" O ASP G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 73 removed outlier: 3.629A pdb=" N ALA G 73 " --> pdb=" O ASP G 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 70 through 73' Processing helix chain 'G' and resid 102 through 118 Processing helix chain 'G' and resid 188 through 201 Processing helix chain 'G' and resid 227 through 248 Processing helix chain 'G' and resid 290 through 303 Processing helix chain 'G' and resid 303 through 312 removed outlier: 4.340A pdb=" N GLY G 309 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE G 310 " --> pdb=" O ALA G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 319 removed outlier: 3.785A pdb=" N TYR G 318 " --> pdb=" O THR G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 383 Processing helix chain 'G' and resid 412 through 424 removed outlier: 3.694A pdb=" N LYS G 422 " --> pdb=" O GLU G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 429 removed outlier: 3.715A pdb=" N LYS G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 454 Processing helix chain 'G' and resid 457 through 465 Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 35 through 37 No H-bonds generated for 'chain 'H' and resid 35 through 37' Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 102 through 118 removed outlier: 3.820A pdb=" N GLY H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 201 Processing helix chain 'H' and resid 227 through 248 Processing helix chain 'H' and resid 293 through 303 Processing helix chain 'H' and resid 303 through 312 removed outlier: 4.108A pdb=" N GLY H 309 " --> pdb=" O LYS H 305 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE H 310 " --> pdb=" O ALA H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 320 Processing helix chain 'H' and resid 365 through 384 Processing helix chain 'H' and resid 412 through 423 Processing helix chain 'H' and resid 424 through 429 Processing helix chain 'H' and resid 430 through 432 No H-bonds generated for 'chain 'H' and resid 430 through 432' Processing helix chain 'H' and resid 434 through 454 Processing helix chain 'H' and resid 457 through 465 removed outlier: 3.596A pdb=" N TYR H 461 " --> pdb=" O HIS H 457 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR H 465 " --> pdb=" O TYR H 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 12 Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 102 through 118 removed outlier: 3.733A pdb=" N GLY I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 159 removed outlier: 3.875A pdb=" N THR I 159 " --> pdb=" O ALA I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'I' and resid 227 through 248 removed outlier: 3.587A pdb=" N TYR I 248 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 303 Processing helix chain 'I' and resid 303 through 312 removed outlier: 3.763A pdb=" N GLY I 309 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE I 310 " --> pdb=" O ALA I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 321 Processing helix chain 'I' and resid 349 through 353 removed outlier: 3.858A pdb=" N ARG I 353 " --> pdb=" O PRO I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 384 Processing helix chain 'I' and resid 412 through 424 Processing helix chain 'I' and resid 434 through 454 Processing helix chain 'I' and resid 457 through 465 removed outlier: 3.674A pdb=" N TYR I 465 " --> pdb=" O TYR I 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 12 Processing helix chain 'J' and resid 35 through 37 No H-bonds generated for 'chain 'J' and resid 35 through 37' Processing helix chain 'J' and resid 38 through 45 Processing helix chain 'J' and resid 70 through 73 Processing helix chain 'J' and resid 102 through 118 removed outlier: 3.719A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 159 removed outlier: 3.887A pdb=" N THR J 159 " --> pdb=" O ALA J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 201 removed outlier: 3.546A pdb=" N MET J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 248 Processing helix chain 'J' and resid 290 through 303 Processing helix chain 'J' and resid 303 through 312 removed outlier: 4.283A pdb=" N GLY J 309 " --> pdb=" O LYS J 305 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE J 310 " --> pdb=" O ALA J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 320 Processing helix chain 'J' and resid 365 through 383 Processing helix chain 'J' and resid 412 through 423 Processing helix chain 'J' and resid 424 through 429 Processing helix chain 'J' and resid 434 through 454 Processing helix chain 'J' and resid 457 through 465 removed outlier: 3.589A pdb=" N TYR J 461 " --> pdb=" O HIS J 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 12 Processing helix chain 'L' and resid 35 through 37 No H-bonds generated for 'chain 'L' and resid 35 through 37' Processing helix chain 'L' and resid 38 through 45 removed outlier: 3.545A pdb=" N PHE L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 102 through 118 removed outlier: 3.622A pdb=" N GLY L 118 " --> pdb=" O LEU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 159 removed outlier: 3.799A pdb=" N THR L 159 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 201 Processing helix chain 'L' and resid 226 through 248 Processing helix chain 'L' and resid 290 through 303 Processing helix chain 'L' and resid 303 through 312 removed outlier: 4.017A pdb=" N GLY L 309 " --> pdb=" O LYS L 305 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE L 310 " --> pdb=" O ALA L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 320 removed outlier: 3.577A pdb=" N TYR L 318 " --> pdb=" O THR L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 353 Processing helix chain 'L' and resid 365 through 384 Processing helix chain 'L' and resid 412 through 423 Processing helix chain 'L' and resid 434 through 454 Processing helix chain 'L' and resid 457 through 465 Processing helix chain 'K' and resid 3 through 12 Processing helix chain 'K' and resid 35 through 37 No H-bonds generated for 'chain 'K' and resid 35 through 37' Processing helix chain 'K' and resid 38 through 45 removed outlier: 3.565A pdb=" N PHE K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 73 Processing helix chain 'K' and resid 102 through 118 removed outlier: 3.735A pdb=" N GLY K 118 " --> pdb=" O LEU K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 201 removed outlier: 3.505A pdb=" N ARG K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 248 Processing helix chain 'K' and resid 285 through 289 Processing helix chain 'K' and resid 290 through 303 Processing helix chain 'K' and resid 303 through 312 removed outlier: 4.049A pdb=" N GLY K 309 " --> pdb=" O LYS K 305 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE K 310 " --> pdb=" O ALA K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 321 removed outlier: 3.522A pdb=" N ARG K 320 " --> pdb=" O ASN K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 353 Processing helix chain 'K' and resid 365 through 384 Processing helix chain 'K' and resid 412 through 423 Processing helix chain 'K' and resid 424 through 429 removed outlier: 3.504A pdb=" N LYS K 429 " --> pdb=" O ALA K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 430 through 432 No H-bonds generated for 'chain 'K' and resid 430 through 432' Processing helix chain 'K' and resid 434 through 454 Processing helix chain 'K' and resid 457 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 33 current: chain 'A' and resid 65 through 75 removed outlier: 4.691A pdb=" N VAL A 87 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER A 71 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N ILE A 85 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N ALA A 73 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N THR A 83 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 97 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 128 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 225 through 226 current: chain 'A' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 278 through 279 current: chain 'A' and resid 340 through 343 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 142 Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 33 current: chain 'B' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 63 through 68 current: chain 'B' and resid 83 through 91 Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 134 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 121 through 134 current: chain 'B' and resid 217 through 222 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 217 through 222 current: chain 'B' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 278 through 279 current: chain 'B' and resid 340 through 343 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AA9, first strand: chain 'C' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 33 current: chain 'C' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 64 through 68 current: chain 'C' and resid 83 through 92 removed outlier: 3.914A pdb=" N GLN C 97 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 128 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 225 through 226 current: chain 'C' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 278 through 279 current: chain 'C' and resid 355 through 357 Processing sheet with id=AB2, first strand: chain 'C' and resid 205 through 210 Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AB4, first strand: chain 'D' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 27 through 33 current: chain 'D' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 64 through 68 current: chain 'D' and resid 83 through 91 Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 134 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 134 current: chain 'D' and resid 218 through 222 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 218 through 222 current: chain 'D' and resid 342 through 343 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 142 Processing sheet with id=AB7, first strand: chain 'D' and resid 274 through 275 Processing sheet with id=AB8, first strand: chain 'F' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 27 through 33 current: chain 'F' and resid 64 through 69 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 64 through 69 current: chain 'F' and resid 83 through 92 removed outlier: 3.859A pdb=" N GLN F 97 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 225 through 226 removed outlier: 3.539A pdb=" N ASN F 225 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 274 " --> pdb=" O ASP F 121 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA F 123 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER F 272 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE F 125 " --> pdb=" O HIS F 270 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS F 270 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS F 268 " --> pdb=" O PRO F 127 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET F 330 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ARG F 343 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N ALA F 332 " --> pdb=" O ARG F 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 205 through 210 removed outlier: 6.602A pdb=" N GLY F 221 " --> pdb=" O GLU F 206 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS F 208 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU F 219 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N HIS F 210 " --> pdb=" O GLN F 217 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLN F 217 " --> pdb=" O HIS F 210 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 136 through 142 removed outlier: 5.505A pdb=" N SER F 146 " --> pdb=" O PHE L 148 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE L 148 " --> pdb=" O SER F 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 27 through 33 removed outlier: 6.926A pdb=" N TRP E 15 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 86 " --> pdb=" O TRP E 15 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP E 17 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS E 88 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG E 19 " --> pdb=" O CYS E 88 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE E 90 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N THR E 21 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR E 83 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 87 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR E 72 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N ASP E 89 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N ASP E 70 " --> pdb=" O ASP E 89 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 128 removed outlier: 4.936A pdb=" N ALA E 340 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA E 332 " --> pdb=" O ALA E 340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 205 through 210 Processing sheet with id=AC6, first strand: chain 'E' and resid 136 through 142 Processing sheet with id=AC7, first strand: chain 'E' and resid 274 through 275 Processing sheet with id=AC8, first strand: chain 'G' and resid 15 through 20 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 28 through 33 current: chain 'G' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 64 through 68 current: chain 'G' and resid 83 through 91 Processing sheet with id=AC9, first strand: chain 'G' and resid 121 through 128 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 225 through 226 current: chain 'G' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 278 through 279 current: chain 'G' and resid 340 through 343 Processing sheet with id=AD1, first strand: chain 'G' and resid 205 through 210 Processing sheet with id=AD2, first strand: chain 'H' and resid 27 through 33 removed outlier: 5.703A pdb=" N THR H 21 " --> pdb=" O CYS H 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 87 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR H 72 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 11.662A pdb=" N ASP H 89 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N ASP H 70 " --> pdb=" O ASP H 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 121 through 134 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 121 through 134 current: chain 'H' and resid 217 through 222 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 217 through 222 current: chain 'H' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 278 through 279 current: chain 'H' and resid 340 through 343 Processing sheet with id=AD4, first strand: chain 'H' and resid 136 through 141 Processing sheet with id=AD5, first strand: chain 'I' and resid 27 through 33 Processing sheet with id=AD6, first strand: chain 'I' and resid 91 through 92 removed outlier: 3.681A pdb=" N GLN I 97 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 121 through 134 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 121 through 134 current: chain 'I' and resid 217 through 222 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 217 through 222 current: chain 'I' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 278 through 279 current: chain 'I' and resid 342 through 343 Processing sheet with id=AD8, first strand: chain 'J' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 27 through 33 current: chain 'J' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 64 through 68 current: chain 'J' and resid 83 through 92 removed outlier: 3.855A pdb=" N GLN J 97 " --> pdb=" O GLU J 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 121 through 128 removed outlier: 3.553A pdb=" N ASN J 225 " --> pdb=" O PHE J 125 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 225 through 226 current: chain 'J' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 278 through 279 current: chain 'J' and resid 340 through 343 Processing sheet with id=AE1, first strand: chain 'J' and resid 205 through 210 Processing sheet with id=AE2, first strand: chain 'L' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 27 through 33 current: chain 'L' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 64 through 68 current: chain 'L' and resid 83 through 91 Processing sheet with id=AE3, first strand: chain 'L' and resid 123 through 134 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 123 through 134 current: chain 'L' and resid 217 through 222 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 217 through 222 current: chain 'L' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 278 through 279 current: chain 'L' and resid 342 through 343 Processing sheet with id=AE4, first strand: chain 'K' and resid 15 through 21 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 27 through 33 current: chain 'K' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 63 through 68 current: chain 'K' and resid 83 through 91 Processing sheet with id=AE5, first strand: chain 'K' and resid 121 through 129 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 225 through 226 current: chain 'K' and resid 278 through 279 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 278 through 279 current: chain 'K' and resid 340 through 343 Processing sheet with id=AE6, first strand: chain 'K' and resid 205 through 210 removed outlier: 3.830A pdb=" N VAL K 207 " --> pdb=" O GLY K 221 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 136 through 142 1679 hydrogen bonds defined for protein. 4779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.25 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7474 1.32 - 1.45: 10215 1.45 - 1.57: 22729 1.57 - 1.69: 0 1.69 - 1.81: 350 Bond restraints: 40768 Sorted by residual: bond pdb=" C PRO L 180 " pdb=" O PRO L 180 " ideal model delta sigma weight residual 1.233 1.203 0.030 9.90e-03 1.02e+04 8.88e+00 bond pdb=" N PRO I 180 " pdb=" CA PRO I 180 " ideal model delta sigma weight residual 1.465 1.435 0.030 1.11e-02 8.12e+03 7.37e+00 bond pdb=" C PRO I 180 " pdb=" O PRO I 180 " ideal model delta sigma weight residual 1.232 1.206 0.026 1.09e-02 8.42e+03 5.90e+00 bond pdb=" N PRO L 180 " pdb=" CA PRO L 180 " ideal model delta sigma weight residual 1.467 1.440 0.027 1.13e-02 7.83e+03 5.82e+00 bond pdb=" C PRO L 182 " pdb=" N PRO L 183 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.83e+00 ... (remaining 40763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 54069 1.68 - 3.35: 801 3.35 - 5.03: 128 5.03 - 6.71: 39 6.71 - 8.38: 5 Bond angle restraints: 55042 Sorted by residual: angle pdb=" N PRO J 182 " pdb=" CA PRO J 182 " pdb=" C PRO J 182 " ideal model delta sigma weight residual 110.70 115.45 -4.75 1.22e+00 6.72e-01 1.52e+01 angle pdb=" N PRO I 182 " pdb=" CA PRO I 182 " pdb=" C PRO I 182 " ideal model delta sigma weight residual 110.70 115.10 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N PRO C 182 " pdb=" CA PRO C 182 " pdb=" C PRO C 182 " ideal model delta sigma weight residual 110.70 115.00 -4.30 1.22e+00 6.72e-01 1.24e+01 angle pdb=" N PRO L 182 " pdb=" CA PRO L 182 " pdb=" C PRO L 182 " ideal model delta sigma weight residual 110.70 114.77 -4.07 1.22e+00 6.72e-01 1.11e+01 angle pdb=" N PRO I 180 " pdb=" CA PRO I 180 " pdb=" C PRO I 180 " ideal model delta sigma weight residual 112.01 105.91 6.10 1.84e+00 2.95e-01 1.10e+01 ... (remaining 55037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20843 17.98 - 35.96: 2704 35.96 - 53.94: 659 53.94 - 71.92: 100 71.92 - 89.90: 48 Dihedral angle restraints: 24354 sinusoidal: 9783 harmonic: 14571 Sorted by residual: dihedral pdb=" CA PHE A 179 " pdb=" C PHE A 179 " pdb=" N PRO A 180 " pdb=" CA PRO A 180 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PHE K 179 " pdb=" C PHE K 179 " pdb=" N PRO K 180 " pdb=" CA PRO K 180 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE J 179 " pdb=" C PHE J 179 " pdb=" N PRO J 180 " pdb=" CA PRO J 180 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 24351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5122 0.063 - 0.127: 742 0.127 - 0.190: 42 0.190 - 0.254: 0 0.254 - 0.317: 1 Chirality restraints: 5907 Sorted by residual: chirality pdb=" CB VAL I 181 " pdb=" CA VAL I 181 " pdb=" CG1 VAL I 181 " pdb=" CG2 VAL I 181 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA VAL L 181 " pdb=" N VAL L 181 " pdb=" C VAL L 181 " pdb=" CB VAL L 181 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA VAL I 181 " pdb=" N VAL I 181 " pdb=" C VAL I 181 " pdb=" CB VAL I 181 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 5904 not shown) Planarity restraints: 7190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE J 179 " 0.075 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO J 180 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO J 180 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO J 180 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 179 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO A 180 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE K 179 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO K 180 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO K 180 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 180 " -0.057 5.00e-02 4.00e+02 ... (remaining 7187 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 672 2.64 - 3.20: 36706 3.20 - 3.77: 65537 3.77 - 4.33: 92352 4.33 - 4.90: 153466 Nonbonded interactions: 348733 Sorted by model distance: nonbonded pdb=" OG SER D 317 " pdb=" OD2 ASP D 361 " model vdw 2.073 3.040 nonbonded pdb=" NZ LYS B 319 " pdb=" OE2 GLU J 460 " model vdw 2.078 3.120 nonbonded pdb=" O PRO C 258 " pdb=" OH TYR I 461 " model vdw 2.129 3.040 nonbonded pdb=" OH TYR C 178 " pdb=" OD1 ASP D 49 " model vdw 2.136 3.040 nonbonded pdb=" OG SER E 317 " pdb=" OD2 ASP E 361 " model vdw 2.137 3.040 ... (remaining 348728 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 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 321 or resid 332 through 335 or resid 341 through 345 or \ resid 354 through 425 or resid 433 through 466)) selection = (chain 'B' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 321 or resid 332 through 335 or resid 341 through 345 or \ resid 354 through 387 or resid 407 through 425 or resid 433 through 466)) selection = (chain 'C' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 321 or resid 332 through 345 or resid 354 through 387 or \ resid 407 through 425 or resid 433 through 466)) selection = (chain 'D' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 161 or resid 167 through 172 or resid 189 through 275 or resid 278 thr \ ough 281 or resid 294 through 321 or resid 332 through 335 or resid 341 through \ 345 or resid 354 through 387 or resid 407 through 425 or resid 433 through 466)) \ selection = (chain 'E' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 321 or resid 332 through 335 or resid 341 through 345 or \ resid 354 through 425 or resid 433 through 466)) selection = (chain 'F' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 281 or resid 294 through 32 \ 1 or resid 332 through 335 or resid 341 through 345 or resid 354 through 387 or \ resid 407 through 425 or resid 433 through 466)) selection = (chain 'G' and (resid 2 through 46 or resid 66 or resid 72 through 77 or resid 8 \ 2 through 116 or resid 124 through 161 or resid 167 through 172 or resid 189 thr \ ough 212 or resid 217 through 275 or resid 278 through 281 or resid 294 through \ 321 or resid 332 through 335 or resid 341 through 345 or resid 354 through 387 o \ r resid 407 through 425 or resid 433 through 466)) selection = (chain 'H' and (resid 2 through 24 or resid 27 through 66 or resid 72 through 77 \ or resid 82 through 116 or resid 124 through 172 or resid 189 through 212 or re \ sid 217 through 275 or resid 278 through 281 or resid 294 through 321 or resid 3 \ 32 through 335 or resid 341 through 345 or resid 354 through 387 or resid 407 th \ rough 425 or resid 433 through 466)) selection = (chain 'I' and (resid 2 through 24 or resid 27 through 46 or resid 66 through 77 \ or resid 82 through 116 or resid 124 through 161 or resid 167 through 172 or re \ sid 189 through 212 or resid 217 through 275 or resid 278 through 281 or resid 2 \ 94 through 321 or resid 332 through 335 or resid 341 through 345 or resid 354 th \ rough 387 or resid 407 through 425 or resid 433 through 466)) selection = (chain 'J' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 321 or resid 332 through 335 or resid 341 through 345 or \ resid 354 through 387 or resid 407 through 425 or resid 433 through 466)) selection = (chain 'K' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 321 or resid 332 through 335 or resid 341 through 345 or \ resid 354 through 387 or resid 407 through 425 or resid 433 through 466)) selection = (chain 'L' and (resid 2 through 24 or resid 27 through 46 or resid 66 or resid 7 \ 2 through 77 or resid 82 through 116 or resid 124 through 161 or resid 167 throu \ gh 172 or resid 189 through 212 or resid 217 through 275 or resid 278 through 28 \ 1 or resid 294 through 335 or resid 341 through 345 or resid 354 through 387 or \ resid 407 through 425 or resid 433 through 466)) } 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: 15.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 39.210 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.003 0.041 40768 Z= 0.142 Angle : 0.533 8.385 55042 Z= 0.283 Chirality : 0.043 0.317 5907 Planarity : 0.005 0.112 7190 Dihedral : 16.956 89.899 14988 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.21 % Allowed : 24.62 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.12), residues: 4920 helix: 1.53 (0.11), residues: 1888 sheet: -0.66 (0.17), residues: 993 loop : -0.23 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.037 0.002 TYR I 239 PHE 0.034 0.001 PHE D 179 TRP 0.006 0.001 TRP L 15 HIS 0.004 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00324 (40768) covalent geometry : angle 0.53256 (55042) hydrogen bonds : bond 0.12264 ( 1679) hydrogen bonds : angle 6.49473 ( 4779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 473 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8697 (mmmt) REVERT: B 96 MET cc_start: 0.7946 (tpt) cc_final: 0.7589 (tpp) REVERT: H 22 ASP cc_start: 0.8420 (p0) cc_final: 0.8135 (p0) REVERT: H 355 ILE cc_start: 0.8988 (mm) cc_final: 0.8688 (pt) REVERT: J 379 ASP cc_start: 0.7348 (t70) cc_final: 0.6903 (t0) outliers start: 9 outliers final: 3 residues processed: 477 average time/residue: 0.2539 time to fit residues: 199.8362 Evaluate side-chains 441 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 438 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 452 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 255 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0570 chunk 494 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** H 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 HIS ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103247 restraints weight = 71662.759| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.11 r_work: 0.3246 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40768 Z= 0.137 Angle : 0.519 7.720 55042 Z= 0.275 Chirality : 0.044 0.256 5907 Planarity : 0.005 0.089 7190 Dihedral : 4.153 31.843 5420 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.86 % Allowed : 22.27 % Favored : 74.87 % 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 (0.12), residues: 4920 helix: 1.74 (0.12), residues: 1899 sheet: -0.68 (0.18), residues: 975 loop : -0.15 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.037 0.001 TYR B 295 PHE 0.030 0.001 PHE D 179 TRP 0.006 0.001 TRP F 157 HIS 0.004 0.001 HIS J 208 Details of bonding type rmsd covalent geometry : bond 0.00319 (40768) covalent geometry : angle 0.51877 (55042) hydrogen bonds : bond 0.03881 ( 1679) hydrogen bonds : angle 5.27382 ( 4779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 485 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: B 96 MET cc_start: 0.7920 (tpt) cc_final: 0.7604 (tpp) REVERT: F 128 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7881 (pt0) REVERT: E 10 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: E 314 SER cc_start: 0.8379 (t) cc_final: 0.7881 (p) REVERT: G 343 ARG cc_start: 0.7599 (mmm160) cc_final: 0.7393 (mmm160) REVERT: G 449 GLU cc_start: 0.6202 (tp30) cc_final: 0.5858 (tp30) REVERT: H 22 ASP cc_start: 0.8369 (p0) cc_final: 0.8002 (p0) REVERT: H 355 ILE cc_start: 0.8859 (mm) cc_final: 0.8627 (pt) REVERT: H 462 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: I 115 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8377 (mppt) REVERT: J 43 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8163 (tp30) REVERT: J 147 MET cc_start: 0.8731 (tmm) cc_final: 0.8435 (tmm) REVERT: J 206 GLU cc_start: 0.7737 (mp0) cc_final: 0.7263 (mp0) REVERT: J 379 ASP cc_start: 0.7498 (t70) cc_final: 0.7062 (t0) REVERT: L 46 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7869 (mtmt) REVERT: L 295 TYR cc_start: 0.8345 (m-10) cc_final: 0.7894 (m-80) REVERT: K 67 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8132 (tpp) REVERT: K 148 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (t80) outliers start: 122 outliers final: 51 residues processed: 585 average time/residue: 0.2401 time to fit residues: 234.6920 Evaluate side-chains 493 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 435 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 461 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 462 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 169 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 158 ASN D 196 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN I 6 GLN ** J 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096590 restraints weight = 73760.043| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.04 r_work: 0.3132 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 40768 Z= 0.356 Angle : 0.683 10.199 55042 Z= 0.362 Chirality : 0.050 0.299 5907 Planarity : 0.006 0.106 7190 Dihedral : 4.844 39.515 5415 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.65 % Favored : 95.33 % Rotamer: Outliers : 4.83 % Allowed : 21.43 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: 0.04 (0.12), residues: 4920 helix: 1.26 (0.11), residues: 1894 sheet: -1.09 (0.17), residues: 1012 loop : -0.43 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 353 TYR 0.025 0.002 TYR B 260 PHE 0.045 0.002 PHE L 148 TRP 0.011 0.002 TRP B 15 HIS 0.011 0.002 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00841 (40768) covalent geometry : angle 0.68296 (55042) hydrogen bonds : bond 0.04839 ( 1679) hydrogen bonds : angle 5.51393 ( 4779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 425 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8698 (mmm) cc_final: 0.8452 (mpp) REVERT: A 148 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7665 (t80) REVERT: A 338 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5701 (mtm-85) REVERT: B 7 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 28 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8713 (mm-40) REVERT: D 194 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7499 (mtt) REVERT: D 344 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7423 (mm) REVERT: F 315 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7390 (p) REVERT: G 24 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7338 (mtpt) REVERT: I 27 GLN cc_start: 0.5535 (OUTLIER) cc_final: 0.4700 (pt0) REVERT: J 43 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8164 (tp30) REVERT: J 80 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: J 148 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7630 (t80) REVERT: J 189 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: J 206 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: J 379 ASP cc_start: 0.7699 (t70) cc_final: 0.7282 (t0) REVERT: L 46 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7841 (mtmt) REVERT: L 168 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8263 (mmtm) REVERT: K 67 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8224 (tpp) outliers start: 206 outliers final: 113 residues processed: 589 average time/residue: 0.2455 time to fit residues: 241.6877 Evaluate side-chains 537 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 408 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 461 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 452 VAL Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 311 THR Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 467 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 290 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 447 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 375 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 378 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 412 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 243 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** J 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101178 restraints weight = 71756.696| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.01 r_work: 0.3214 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40768 Z= 0.135 Angle : 0.528 6.950 55042 Z= 0.279 Chirality : 0.044 0.252 5907 Planarity : 0.005 0.085 7190 Dihedral : 4.404 37.521 5415 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 3.45 % Allowed : 22.62 % Favored : 73.93 % 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: 0.37 (0.12), residues: 4920 helix: 1.55 (0.11), residues: 1903 sheet: -1.00 (0.17), residues: 988 loop : -0.24 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.025 0.002 TYR B 295 PHE 0.033 0.001 PHE L 148 TRP 0.006 0.001 TRP I 157 HIS 0.004 0.001 HIS J 208 Details of bonding type rmsd covalent geometry : bond 0.00317 (40768) covalent geometry : angle 0.52817 (55042) hydrogen bonds : bond 0.03830 ( 1679) hydrogen bonds : angle 5.13919 ( 4779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 456 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8661 (mmm) cc_final: 0.8457 (mpp) REVERT: B 96 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7618 (tpp) REVERT: B 295 TYR cc_start: 0.7718 (m-80) cc_final: 0.7518 (m-80) REVERT: B 336 ARG cc_start: 0.6274 (tpt170) cc_final: 0.5997 (tpt170) REVERT: D 175 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7864 (tmtt) REVERT: D 194 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7554 (mtt) REVERT: E 314 SER cc_start: 0.8318 (t) cc_final: 0.7883 (p) REVERT: G 24 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7339 (mtpt) REVERT: H 146 SER cc_start: 0.6163 (OUTLIER) cc_final: 0.5935 (t) REVERT: H 462 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: I 291 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7905 (t70) REVERT: J 43 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8156 (tp30) REVERT: J 80 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: J 148 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7728 (t80) REVERT: J 189 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: J 379 ASP cc_start: 0.7631 (t70) cc_final: 0.7241 (t0) REVERT: L 46 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7777 (mtmt) REVERT: L 295 TYR cc_start: 0.8391 (m-10) cc_final: 0.7931 (m-80) REVERT: K 43 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8088 (mm-30) REVERT: K 67 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: K 148 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8687 (t80) outliers start: 147 outliers final: 74 residues processed: 577 average time/residue: 0.2439 time to fit residues: 234.7016 Evaluate side-chains 513 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 426 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 461 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 462 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 467 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 17 optimal weight: 0.8980 chunk 431 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN ** J 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099885 restraints weight = 72065.112| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.10 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40768 Z= 0.183 Angle : 0.546 6.968 55042 Z= 0.289 Chirality : 0.045 0.247 5907 Planarity : 0.005 0.081 7190 Dihedral : 4.380 36.930 5415 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 3.99 % Allowed : 21.99 % Favored : 74.02 % 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: 0.35 (0.12), residues: 4920 helix: 1.56 (0.11), residues: 1902 sheet: -1.05 (0.17), residues: 1012 loop : -0.25 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.028 0.002 TYR I 239 PHE 0.028 0.002 PHE F 41 TRP 0.007 0.001 TRP I 157 HIS 0.007 0.001 HIS L 186 Details of bonding type rmsd covalent geometry : bond 0.00437 (40768) covalent geometry : angle 0.54580 (55042) hydrogen bonds : bond 0.03929 ( 1679) hydrogen bonds : angle 5.10100 ( 4779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 435 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: A 96 MET cc_start: 0.8676 (mmm) cc_final: 0.8419 (mpp) REVERT: B 7 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 96 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7617 (tpp) REVERT: B 295 TYR cc_start: 0.7717 (m-80) cc_final: 0.7514 (m-80) REVERT: D 175 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (tmtt) REVERT: D 194 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7530 (mtt) REVERT: G 24 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7360 (mtpt) REVERT: H 146 SER cc_start: 0.6236 (OUTLIER) cc_final: 0.5922 (t) REVERT: H 462 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: I 291 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7900 (t70) REVERT: J 43 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8200 (tp30) REVERT: J 80 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: J 148 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7739 (t80) REVERT: J 206 GLU cc_start: 0.7813 (mp0) cc_final: 0.7277 (mp0) REVERT: J 222 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8536 (m) REVERT: J 379 ASP cc_start: 0.7688 (t70) cc_final: 0.7252 (t0) REVERT: L 46 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7721 (mtmt) REVERT: L 295 TYR cc_start: 0.8411 (m-10) cc_final: 0.8088 (m-80) REVERT: K 43 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8124 (mm-30) REVERT: K 67 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8284 (tpp) outliers start: 170 outliers final: 113 residues processed: 575 average time/residue: 0.2396 time to fit residues: 229.7938 Evaluate side-chains 549 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 422 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 461 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 462 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 311 THR Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 409 VAL Chi-restraints excluded: chain I residue 467 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 426 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 chunk 373 optimal weight: 0.9980 chunk 363 optimal weight: 8.9990 chunk 315 optimal weight: 0.9980 chunk 417 optimal weight: 10.0000 chunk 412 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN ** J 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102027 restraints weight = 72901.627| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.07 r_work: 0.3236 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 40768 Z= 0.154 Angle : 0.525 6.796 55042 Z= 0.277 Chirality : 0.044 0.245 5907 Planarity : 0.005 0.073 7190 Dihedral : 4.272 35.520 5415 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 3.94 % Allowed : 22.13 % Favored : 73.93 % 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: 0.45 (0.12), residues: 4920 helix: 1.65 (0.11), residues: 1905 sheet: -1.02 (0.17), residues: 1007 loop : -0.19 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 108 TYR 0.022 0.001 TYR I 239 PHE 0.027 0.001 PHE F 359 TRP 0.006 0.001 TRP I 157 HIS 0.004 0.001 HIS J 208 Details of bonding type rmsd covalent geometry : bond 0.00364 (40768) covalent geometry : angle 0.52463 (55042) hydrogen bonds : bond 0.03752 ( 1679) hydrogen bonds : angle 5.00333 ( 4779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 458 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: A 96 MET cc_start: 0.8674 (mmm) cc_final: 0.8428 (mpp) REVERT: A 338 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5614 (mtm-85) REVERT: B 7 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8029 (mp) REVERT: B 96 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7631 (tpp) REVERT: B 154 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: B 461 TYR cc_start: 0.9016 (m-80) cc_final: 0.8668 (m-80) REVERT: D 175 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7899 (tmtt) REVERT: F 315 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.6979 (p) REVERT: E 314 SER cc_start: 0.8414 (t) cc_final: 0.7983 (p) REVERT: E 408 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: G 24 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7384 (mtpt) REVERT: G 80 GLU cc_start: 0.8183 (mp0) cc_final: 0.7831 (mm-30) REVERT: H 146 SER cc_start: 0.6210 (OUTLIER) cc_final: 0.5942 (t) REVERT: H 462 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: I 291 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7878 (t70) REVERT: J 43 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8156 (tp30) REVERT: J 80 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: J 148 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7789 (t80) REVERT: J 206 GLU cc_start: 0.7759 (mp0) cc_final: 0.7165 (mp0) REVERT: J 222 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8425 (m) REVERT: J 379 ASP cc_start: 0.7616 (t70) cc_final: 0.7187 (t0) REVERT: L 46 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7737 (mtmt) REVERT: K 43 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8203 (mm-30) REVERT: K 67 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: K 148 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8690 (t80) outliers start: 168 outliers final: 119 residues processed: 597 average time/residue: 0.2483 time to fit residues: 246.6174 Evaluate side-chains 559 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 422 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 461 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 408 GLN Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 462 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 311 THR Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 409 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 307 optimal weight: 7.9990 chunk 118 optimal weight: 0.0980 chunk 471 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 365 optimal weight: 0.8980 chunk 406 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 HIS ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 408 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100807 restraints weight = 72919.704| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.05 r_work: 0.3218 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 40768 Z= 0.198 Angle : 0.556 7.391 55042 Z= 0.295 Chirality : 0.045 0.241 5907 Planarity : 0.005 0.090 7190 Dihedral : 4.367 35.789 5415 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.15 % Allowed : 22.27 % Favored : 73.57 % 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: 0.35 (0.12), residues: 4920 helix: 1.59 (0.11), residues: 1902 sheet: -1.07 (0.17), residues: 1015 loop : -0.25 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 19 TYR 0.068 0.002 TYR B 295 PHE 0.039 0.002 PHE L 148 TRP 0.007 0.001 TRP I 157 HIS 0.006 0.001 HIS L 208 Details of bonding type rmsd covalent geometry : bond 0.00472 (40768) covalent geometry : angle 0.55639 (55042) hydrogen bonds : bond 0.03928 ( 1679) hydrogen bonds : angle 5.05351 ( 4779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 429 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: A 96 MET cc_start: 0.8663 (mmm) cc_final: 0.8398 (mpp) REVERT: A 338 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5681 (mtm-85) REVERT: B 7 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 96 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7657 (tpp) REVERT: B 154 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8577 (pt0) REVERT: F 212 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8785 (m) REVERT: F 315 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7132 (p) REVERT: E 408 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: G 24 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7348 (mtpt) REVERT: H 146 SER cc_start: 0.6296 (OUTLIER) cc_final: 0.6021 (t) REVERT: H 148 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7288 (t80) REVERT: I 291 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7883 (t70) REVERT: J 43 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8158 (tp30) REVERT: J 80 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: J 148 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7766 (t80) REVERT: J 379 ASP cc_start: 0.7683 (t70) cc_final: 0.7258 (t0) REVERT: L 46 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7761 (mtmt) REVERT: K 43 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8205 (mm-30) REVERT: K 67 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8325 (tpp) outliers start: 177 outliers final: 133 residues processed: 579 average time/residue: 0.2484 time to fit residues: 239.3308 Evaluate side-chains 568 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 419 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 461 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 408 GLN Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 148 PHE Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 311 THR Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 409 VAL Chi-restraints excluded: chain I residue 467 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 290 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 459 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 459 LEU Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 176 optimal weight: 8.9990 chunk 462 optimal weight: 4.9990 chunk 497 optimal weight: 0.9980 chunk 325 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 297 optimal weight: 0.2980 chunk 371 optimal weight: 7.9990 chunk 314 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 chunk 337 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN C 308 ASN C 316 ASN D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 GLN H 386 HIS I 268 HIS J 218 ASN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104432 restraints weight = 71165.990| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.01 r_work: 0.3259 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40768 Z= 0.111 Angle : 0.502 6.716 55042 Z= 0.266 Chirality : 0.043 0.209 5907 Planarity : 0.005 0.082 7190 Dihedral : 4.117 32.269 5415 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.07 % Allowed : 23.35 % Favored : 73.57 % 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: 0.59 (0.12), residues: 4920 helix: 1.78 (0.12), residues: 1910 sheet: -0.98 (0.17), residues: 994 loop : -0.10 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.056 0.001 TYR B 295 PHE 0.031 0.001 PHE F 359 TRP 0.007 0.001 TRP F 157 HIS 0.004 0.001 HIS L 186 Details of bonding type rmsd covalent geometry : bond 0.00254 (40768) covalent geometry : angle 0.50239 (55042) hydrogen bonds : bond 0.03455 ( 1679) hydrogen bonds : angle 4.86331 ( 4779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 490 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: A 96 MET cc_start: 0.8609 (mmm) cc_final: 0.8397 (mpp) REVERT: B 7 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 96 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7573 (tpp) REVERT: B 154 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: C 160 ASP cc_start: 0.9086 (p0) cc_final: 0.8785 (p0) REVERT: C 439 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: E 10 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: E 314 SER cc_start: 0.8305 (t) cc_final: 0.7828 (p) REVERT: G 23 THR cc_start: 0.7193 (OUTLIER) cc_final: 0.6859 (m) REVERT: G 80 GLU cc_start: 0.8194 (mp0) cc_final: 0.7820 (mm-30) REVERT: G 206 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7593 (mp0) REVERT: G 462 ASP cc_start: 0.8931 (t70) cc_final: 0.8730 (t0) REVERT: H 22 ASP cc_start: 0.8508 (p0) cc_final: 0.8131 (p0) REVERT: H 96 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: H 146 SER cc_start: 0.6037 (OUTLIER) cc_final: 0.5792 (t) REVERT: H 171 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8294 (ptp90) REVERT: H 355 ILE cc_start: 0.8915 (mm) cc_final: 0.8574 (pt) REVERT: I 291 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7915 (t70) REVERT: J 43 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8158 (tp30) REVERT: J 80 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: J 148 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7797 (t80) REVERT: J 379 ASP cc_start: 0.7596 (t70) cc_final: 0.7150 (t0) REVERT: L 46 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7691 (mtmt) REVERT: K 43 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8096 (mm-30) REVERT: K 67 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8210 (tpp) outliers start: 131 outliers final: 86 residues processed: 589 average time/residue: 0.2461 time to fit residues: 241.6393 Evaluate side-chains 538 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 437 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 218 ASN Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 459 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 255 MET Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 459 LEU Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 346 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 371 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 497 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 HIS D 97 GLN D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 ASN J 218 ASN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102177 restraints weight = 71972.073| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.01 r_work: 0.3221 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40768 Z= 0.165 Angle : 0.542 12.229 55042 Z= 0.285 Chirality : 0.045 0.224 5907 Planarity : 0.005 0.111 7190 Dihedral : 4.189 32.631 5415 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.91 % Allowed : 23.73 % Favored : 73.36 % 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: 0.53 (0.12), residues: 4920 helix: 1.73 (0.12), residues: 1911 sheet: -1.00 (0.17), residues: 1013 loop : -0.14 (0.15), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.068 0.002 TYR B 295 PHE 0.030 0.001 PHE F 41 TRP 0.006 0.001 TRP I 157 HIS 0.005 0.001 HIS L 457 Details of bonding type rmsd covalent geometry : bond 0.00393 (40768) covalent geometry : angle 0.54180 (55042) hydrogen bonds : bond 0.03708 ( 1679) hydrogen bonds : angle 4.91543 ( 4779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 441 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: A 96 MET cc_start: 0.8596 (mmm) cc_final: 0.8373 (mpp) REVERT: A 338 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5712 (mtm-85) REVERT: B 7 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 96 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7564 (tpp) REVERT: B 154 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: C 160 ASP cc_start: 0.9091 (p0) cc_final: 0.8785 (p0) REVERT: C 439 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: D 64 MET cc_start: 0.8635 (mmm) cc_final: 0.8132 (mpp) REVERT: F 315 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7157 (p) REVERT: E 10 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: E 314 SER cc_start: 0.8454 (t) cc_final: 0.8015 (p) REVERT: G 24 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7484 (mtpt) REVERT: H 146 SER cc_start: 0.6159 (OUTLIER) cc_final: 0.5923 (t) REVERT: I 291 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7913 (t70) REVERT: J 43 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8199 (tp30) REVERT: J 80 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: J 148 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7858 (t80) REVERT: J 379 ASP cc_start: 0.7650 (t70) cc_final: 0.7214 (t0) REVERT: L 46 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7733 (mtmt) REVERT: K 43 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8094 (mm-30) REVERT: K 67 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8548 (tpp) outliers start: 124 outliers final: 89 residues processed: 538 average time/residue: 0.2472 time to fit residues: 221.6229 Evaluate side-chains 533 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 429 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 218 ASN Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 459 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 255 MET Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 459 LEU Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 215 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 488 optimal weight: 5.9990 chunk 402 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 427 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN J 218 ASN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100000 restraints weight = 72973.783| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.04 r_work: 0.3205 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 40768 Z= 0.236 Angle : 0.602 10.927 55042 Z= 0.317 Chirality : 0.047 0.252 5907 Planarity : 0.006 0.118 7190 Dihedral : 4.484 35.675 5415 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.84 % Allowed : 23.68 % Favored : 73.48 % 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: 0.33 (0.12), residues: 4920 helix: 1.57 (0.11), residues: 1901 sheet: -1.07 (0.17), residues: 1004 loop : -0.28 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.067 0.002 TYR B 295 PHE 0.031 0.002 PHE F 41 TRP 0.007 0.001 TRP C 157 HIS 0.009 0.001 HIS L 457 Details of bonding type rmsd covalent geometry : bond 0.00562 (40768) covalent geometry : angle 0.60202 (55042) hydrogen bonds : bond 0.04124 ( 1679) hydrogen bonds : angle 5.10851 ( 4779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 426 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: A 96 MET cc_start: 0.8656 (mmm) cc_final: 0.8374 (mpp) REVERT: A 338 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5728 (mtm-85) REVERT: B 96 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7658 (tpp) REVERT: B 154 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8596 (pt0) REVERT: C 160 ASP cc_start: 0.9092 (p0) cc_final: 0.8663 (p0) REVERT: D 64 MET cc_start: 0.8761 (mmm) cc_final: 0.8109 (mpp) REVERT: F 315 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7327 (p) REVERT: E 408 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: G 24 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7320 (mtpt) REVERT: H 146 SER cc_start: 0.6431 (OUTLIER) cc_final: 0.6107 (t) REVERT: I 291 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7876 (t70) REVERT: J 43 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8168 (tp30) REVERT: J 80 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: J 148 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7672 (t80) REVERT: J 379 ASP cc_start: 0.7680 (t70) cc_final: 0.7260 (t0) REVERT: L 46 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7778 (mtmt) REVERT: K 43 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8174 (mm-30) REVERT: K 67 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8322 (tpp) outliers start: 121 outliers final: 101 residues processed: 525 average time/residue: 0.2476 time to fit residues: 216.6323 Evaluate side-chains 529 residues out of total 4261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 415 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 408 GLN Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 291 ASP Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 467 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 218 ASN Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 459 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 255 MET Chi-restraints excluded: chain K residue 456 VAL Chi-restraints excluded: chain K residue 459 LEU Chi-restraints excluded: chain K residue 462 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 116 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 447 optimal weight: 0.9980 chunk 383 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 420 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN J 218 ASN ** L 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103857 restraints weight = 71300.256| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.00 r_work: 0.3263 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40768 Z= 0.116 Angle : 0.522 12.247 55042 Z= 0.275 Chirality : 0.044 0.216 5907 Planarity : 0.005 0.099 7190 Dihedral : 4.169 32.689 5415 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.63 % Allowed : 24.15 % Favored : 73.22 % 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: 0.53 (0.12), residues: 4920 helix: 1.72 (0.12), residues: 1914 sheet: -1.02 (0.17), residues: 1009 loop : -0.12 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.061 0.002 TYR B 295 PHE 0.028 0.001 PHE F 41 TRP 0.008 0.001 TRP B 157 HIS 0.005 0.001 HIS L 186 Details of bonding type rmsd covalent geometry : bond 0.00268 (40768) covalent geometry : angle 0.52217 (55042) hydrogen bonds : bond 0.03526 ( 1679) hydrogen bonds : angle 4.92206 ( 4779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10261.22 seconds wall clock time: 176 minutes 58.25 seconds (10618.25 seconds total)