Starting phenix.real_space_refine on Thu Jul 2 18:07:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl0_36385/07_2026/8jl0_36385.map" } resolution = 3.1 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= 0.002 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 33 5.16 5 C 5757 2.51 5 N 1583 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9244 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4572 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3712 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 440} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'RNA': 22} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 19} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.02, per 1000 atoms: 0.22 Number of scatterers: 9244 At special positions: 0 Unit cell: (84.84, 115.08, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 46 15.00 O 1825 8.00 N 1583 7.00 C 5757 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: 0.95 Conformation dependent library (CDL) restraints added in 325.8 milliseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 41.2% alpha, 17.9% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 3.816A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 4.281A pdb=" N SER A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.515A pdb=" N PHE A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.712A pdb=" N ASN A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.518A pdb=" N LYS A 260 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.851A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.528A pdb=" N ALA A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.607A pdb=" N LYS A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.804A pdb=" N LYS A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.575A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.506A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.762A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 109 through 119 removed outlier: 4.128A pdb=" N HIS B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.950A pdb=" N GLU B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.802A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.615A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 4.206A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 458 removed outlier: 4.069A pdb=" N GLN B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 162 removed outlier: 7.227A pdb=" N MET A 20 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N PHE A 139 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP A 22 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 221 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 254 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 223 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.537A pdb=" N GLY A 582 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER A 580 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 579 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA B 10 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 581 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 12 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 12.386A pdb=" N LEU B 8 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR B 370 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA B 10 " --> pdb=" O PRO B 368 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 223 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS B 306 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 225 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 226 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 246 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 228 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 245 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 258 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 257 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.571A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 438 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.571A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374 removed outlier: 4.932A pdb=" N VAL A 378 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 343 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 404 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 398 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.511A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N CYS B 107 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B 54 " --> pdb=" O CYS B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.511A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG B 51 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 147 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA B 53 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR B 149 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 55 " --> pdb=" O TYR B 149 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1410 1.31 - 1.43: 2851 1.43 - 1.56: 5155 1.56 - 1.69: 94 1.69 - 1.81: 51 Bond restraints: 9561 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.247 0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.678 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.280 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.268 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 9556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 12964 2.58 - 5.17: 178 5.17 - 7.75: 20 7.75 - 10.33: 2 10.33 - 12.91: 4 Bond angle restraints: 13168 Sorted by residual: angle pdb=" N PRO A 329 " pdb=" CA PRO A 329 " pdb=" C PRO A 329 " ideal model delta sigma weight residual 112.47 100.45 12.02 2.06e+00 2.36e-01 3.41e+01 angle pdb=" C3' A C 1 " pdb=" O3' A C 1 " pdb=" P U C 2 " ideal model delta sigma weight residual 120.20 113.69 6.51 1.50e+00 4.44e-01 1.89e+01 angle pdb=" N3 DT D 20 " pdb=" C4 DT D 20 " pdb=" O4 DT D 20 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.73 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N3 DT D 9 " pdb=" C4 DT D 9 " pdb=" O4 DT D 9 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 13163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.70: 5099 27.70 - 55.41: 521 55.41 - 83.11: 87 83.11 - 110.81: 5 110.81 - 138.51: 2 Dihedral angle restraints: 5714 sinusoidal: 2674 harmonic: 3040 Sorted by residual: dihedral pdb=" O4' C C 17 " pdb=" C1' C C 17 " pdb=" N1 C C 17 " pdb=" C2 C C 17 " ideal model delta sinusoidal sigma weight residual -160.00 -21.49 -138.51 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" N SER A 261 " pdb=" CA SER A 261 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" C4' DC D 2 " pdb=" C3' DC D 2 " pdb=" O3' DC D 2 " pdb=" P DG D 3 " ideal model delta sinusoidal sigma weight residual -140.00 -7.37 -132.63 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1396 0.109 - 0.217: 63 0.217 - 0.326: 2 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" P A C 1 " pdb=" OP1 A C 1 " pdb=" OP2 A C 1 " pdb=" O5' A C 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" P U C 2 " pdb=" OP1 U C 2 " pdb=" OP2 U C 2 " pdb=" O5' U C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1461 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 344 " 0.444 9.50e-02 1.11e+02 1.99e-01 2.43e+01 pdb=" NE ARG A 344 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 344 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 344 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 344 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 414 " 0.016 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER A 414 " -0.052 2.00e-02 2.50e+03 pdb=" O SER A 414 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 415 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 4 " -0.033 2.00e-02 2.50e+03 1.48e-02 6.04e+00 pdb=" N9 A C 4 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A C 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A C 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A C 4 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A C 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A C 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 4 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1543 2.77 - 3.30: 8321 3.30 - 3.83: 15661 3.83 - 4.37: 18393 4.37 - 4.90: 30818 Nonbonded interactions: 74736 Sorted by model distance: nonbonded pdb=" OD1 ASN B 435 " pdb=" OG1 THR B 437 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.237 3.040 nonbonded pdb=" O ARG A 440 " pdb=" OG1 THR A 443 " model vdw 2.246 3.040 nonbonded pdb=" O2D NAD A 601 " pdb=" O3D NAD A 601 " model vdw 2.257 2.432 nonbonded pdb=" OD1 ASN B 436 " pdb=" O2' A C 3 " model vdw 2.273 3.040 ... (remaining 74731 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.008 0.284 9561 Z= 0.449 Angle : 0.742 12.913 13168 Z= 0.457 Chirality : 0.052 0.543 1464 Planarity : 0.006 0.199 1526 Dihedral : 20.611 138.513 3760 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.30 % Favored : 91.31 % Rotamer: Outliers : 0.79 % Allowed : 29.73 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.51 (0.25), residues: 1036 helix: 0.82 (0.28), residues: 358 sheet: -1.02 (0.37), residues: 199 loop : -2.50 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 105 TYR 0.015 0.002 TYR B 341 PHE 0.015 0.001 PHE A 91 TRP 0.013 0.001 TRP B 377 HIS 0.006 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.45 ( 9561) covalent geometry : angle 0.74193 / 0.46 (13168) hydrogen bonds : bond 0.17908 / 12.29 ( 365) hydrogen bonds : angle 6.51777 / 4.43 ( 1046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.342 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 98 average time/residue: 0.1071 time to fit residues: 14.3583 Evaluate side-chains 89 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127059 restraints weight = 11019.966| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.85 r_work: 0.3089 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9561 Z= 0.154 Angle : 0.586 8.126 13168 Z= 0.320 Chirality : 0.043 0.293 1464 Planarity : 0.004 0.032 1526 Dihedral : 17.346 138.842 1788 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.43 % Favored : 92.37 % Rotamer: Outliers : 3.27 % Allowed : 29.39 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.28 (0.25), residues: 1036 helix: 0.92 (0.28), residues: 378 sheet: -0.83 (0.37), residues: 193 loop : -2.44 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 105 TYR 0.017 0.002 TYR A 74 PHE 0.020 0.001 PHE A 328 TRP 0.016 0.001 TRP B 377 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9561) covalent geometry : angle 0.58627 / 0.32 (13168) hydrogen bonds : bond 0.05028 / 3.32 ( 365) hydrogen bonds : angle 5.21154 / 3.54 ( 1046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.342 Fit side-chains REVERT: A 115 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6231 (ptm160) REVERT: A 260 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7764 (mmtp) REVERT: A 426 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7669 (mp) REVERT: B 221 ASP cc_start: 0.7577 (p0) cc_final: 0.7358 (p0) outliers start: 29 outliers final: 10 residues processed: 111 average time/residue: 0.1031 time to fit residues: 15.6364 Evaluate side-chains 95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127343 restraints weight = 11040.571| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.98 r_work: 0.3065 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9561 Z= 0.122 Angle : 0.528 7.926 13168 Z= 0.291 Chirality : 0.041 0.220 1464 Planarity : 0.004 0.029 1526 Dihedral : 17.231 136.812 1787 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 4.50 % Allowed : 28.27 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.06 (0.26), residues: 1036 helix: 1.14 (0.28), residues: 377 sheet: -0.68 (0.38), residues: 187 loop : -2.34 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.014 0.001 TYR A 74 PHE 0.011 0.001 PHE A 80 TRP 0.013 0.001 TRP B 377 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9561) covalent geometry : angle 0.52787 / 0.29 (13168) hydrogen bonds : bond 0.04178 / 2.73 ( 365) hydrogen bonds : angle 4.84709 / 3.29 ( 1046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.345 Fit side-chains REVERT: A 115 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6060 (ptm160) REVERT: A 260 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7784 (mmtp) REVERT: B 221 ASP cc_start: 0.7809 (p0) cc_final: 0.7547 (p0) outliers start: 40 outliers final: 17 residues processed: 128 average time/residue: 0.1042 time to fit residues: 18.4814 Evaluate side-chains 108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 245 ASN A 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.167374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127974 restraints weight = 11143.274| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.03 r_work: 0.3098 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9561 Z= 0.128 Angle : 0.533 8.280 13168 Z= 0.291 Chirality : 0.041 0.223 1464 Planarity : 0.004 0.036 1526 Dihedral : 17.163 138.167 1787 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.34 % Favored : 92.47 % Rotamer: Outliers : 4.39 % Allowed : 28.15 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.99 (0.26), residues: 1036 helix: 1.20 (0.28), residues: 377 sheet: -0.63 (0.39), residues: 187 loop : -2.31 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 168 TYR 0.014 0.001 TYR B 341 PHE 0.013 0.001 PHE B 158 TRP 0.013 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9561) covalent geometry : angle 0.53296 / 0.29 (13168) hydrogen bonds : bond 0.04000 / 2.60 ( 365) hydrogen bonds : angle 4.74498 / 3.23 ( 1046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.361 Fit side-chains REVERT: A 115 ARG cc_start: 0.6453 (OUTLIER) cc_final: 0.6055 (ptm160) REVERT: A 260 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7801 (mmtp) REVERT: B 214 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8548 (mtpt) REVERT: B 221 ASP cc_start: 0.7649 (p0) cc_final: 0.7355 (p0) outliers start: 39 outliers final: 22 residues processed: 123 average time/residue: 0.1169 time to fit residues: 19.5265 Evaluate side-chains 114 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.0030 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.0070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126050 restraints weight = 11120.913| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.31 r_work: 0.3025 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9561 Z= 0.129 Angle : 0.528 7.975 13168 Z= 0.289 Chirality : 0.041 0.214 1464 Planarity : 0.004 0.037 1526 Dihedral : 17.130 138.567 1787 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 5.41 % Allowed : 26.69 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.94 (0.26), residues: 1036 helix: 1.20 (0.28), residues: 378 sheet: -0.60 (0.39), residues: 187 loop : -2.24 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.014 0.001 TYR A 74 PHE 0.010 0.001 PHE A 9 TRP 0.013 0.001 TRP B 377 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9561) covalent geometry : angle 0.52764 / 0.29 (13168) hydrogen bonds : bond 0.03919 / 2.56 ( 365) hydrogen bonds : angle 4.67426 / 3.18 ( 1046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 0.340 Fit side-chains REVERT: A 46 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5031 (t70) REVERT: A 115 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.6098 (ptm160) REVERT: A 260 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7815 (mmtp) REVERT: A 572 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: B 214 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8568 (mtpt) REVERT: B 221 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7350 (p0) REVERT: B 396 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8907 (tttm) outliers start: 48 outliers final: 24 residues processed: 131 average time/residue: 0.1033 time to fit residues: 18.7593 Evaluate side-chains 117 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.166557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126043 restraints weight = 11132.544| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.38 r_work: 0.3028 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9561 Z= 0.135 Angle : 0.533 7.603 13168 Z= 0.291 Chirality : 0.041 0.200 1464 Planarity : 0.004 0.039 1526 Dihedral : 17.122 139.366 1787 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.34 % Favored : 92.57 % Rotamer: Outliers : 4.84 % Allowed : 27.48 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.91 (0.26), residues: 1036 helix: 1.23 (0.28), residues: 377 sheet: -0.55 (0.39), residues: 183 loop : -2.23 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 105 TYR 0.015 0.001 TYR B 341 PHE 0.010 0.001 PHE A 9 TRP 0.014 0.001 TRP B 377 HIS 0.006 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9561) covalent geometry : angle 0.53318 / 0.29 (13168) hydrogen bonds : bond 0.03908 / 2.56 ( 365) hydrogen bonds : angle 4.62876 / 3.15 ( 1046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.342 Fit side-chains REVERT: A 46 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.4942 (t70) REVERT: A 115 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.6044 (ptm160) REVERT: A 260 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7612 (mmtp) REVERT: A 262 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5168 (mp0) REVERT: A 572 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: B 168 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7331 (ttt180) REVERT: B 214 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8573 (mtpt) REVERT: B 221 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7290 (p0) REVERT: B 396 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8893 (tttm) outliers start: 43 outliers final: 27 residues processed: 126 average time/residue: 0.1027 time to fit residues: 17.8193 Evaluate side-chains 124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS B 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123904 restraints weight = 10985.212| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.14 r_work: 0.2952 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9561 Z= 0.175 Angle : 0.574 7.494 13168 Z= 0.311 Chirality : 0.043 0.197 1464 Planarity : 0.004 0.036 1526 Dihedral : 17.192 142.140 1787 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 5.07 % Allowed : 27.25 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.07 (0.26), residues: 1036 helix: 1.08 (0.28), residues: 379 sheet: -0.74 (0.39), residues: 186 loop : -2.27 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 105 TYR 0.019 0.002 TYR B 341 PHE 0.017 0.002 PHE A 9 TRP 0.016 0.001 TRP B 377 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9561) covalent geometry : angle 0.57444 / 0.31 (13168) hydrogen bonds : bond 0.04324 / 2.85 ( 365) hydrogen bonds : angle 4.70793 / 3.20 ( 1046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.264 Fit side-chains REVERT: A 46 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.5352 (t70) REVERT: A 115 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.5976 (ptm160) REVERT: A 133 ASN cc_start: 0.7590 (m-40) cc_final: 0.7238 (m-40) REVERT: A 262 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5267 (mp0) REVERT: A 572 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: B 214 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8564 (mtpt) REVERT: B 221 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7348 (p0) outliers start: 45 outliers final: 26 residues processed: 123 average time/residue: 0.0997 time to fit residues: 16.9705 Evaluate side-chains 119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.0470 chunk 97 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126571 restraints weight = 11059.333| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.29 r_work: 0.3112 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9561 Z= 0.111 Angle : 0.520 6.643 13168 Z= 0.285 Chirality : 0.040 0.155 1464 Planarity : 0.004 0.039 1526 Dihedral : 17.095 137.588 1787 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.05 % Favored : 92.86 % Rotamer: Outliers : 4.17 % Allowed : 28.15 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.26), residues: 1036 helix: 1.28 (0.28), residues: 378 sheet: -0.48 (0.40), residues: 186 loop : -2.17 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 105 TYR 0.014 0.001 TYR B 341 PHE 0.014 0.001 PHE A 328 TRP 0.013 0.001 TRP B 377 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9561) covalent geometry : angle 0.51951 / 0.29 (13168) hydrogen bonds : bond 0.03657 / 2.38 ( 365) hydrogen bonds : angle 4.54677 / 3.10 ( 1046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.298 Fit side-chains REVERT: A 46 HIS cc_start: 0.5772 (OUTLIER) cc_final: 0.5040 (t70) REVERT: A 115 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.6042 (ptm160) REVERT: A 133 ASN cc_start: 0.7425 (m-40) cc_final: 0.7107 (m-40) REVERT: A 260 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7619 (mmtp) REVERT: A 262 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5097 (mp0) REVERT: A 572 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: B 214 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8538 (mtpt) REVERT: B 221 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7365 (p0) outliers start: 37 outliers final: 20 residues processed: 117 average time/residue: 0.1021 time to fit residues: 16.1416 Evaluate side-chains 113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 441 HIS B 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128604 restraints weight = 10972.230| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.91 r_work: 0.3070 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9561 Z= 0.110 Angle : 0.519 7.371 13168 Z= 0.282 Chirality : 0.040 0.152 1464 Planarity : 0.004 0.042 1526 Dihedral : 17.000 136.824 1786 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.05 % Favored : 92.86 % Rotamer: Outliers : 3.83 % Allowed : 28.49 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 1036 helix: 1.34 (0.28), residues: 379 sheet: -0.40 (0.40), residues: 190 loop : -2.11 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 105 TYR 0.013 0.001 TYR B 341 PHE 0.015 0.001 PHE A 91 TRP 0.012 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 9561) covalent geometry : angle 0.51868 / 0.28 (13168) hydrogen bonds : bond 0.03465 / 2.25 ( 365) hydrogen bonds : angle 4.43772 / 3.02 ( 1046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.347 Fit side-chains REVERT: A 46 HIS cc_start: 0.5655 (OUTLIER) cc_final: 0.4937 (t70) REVERT: A 115 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5855 (ptm160) REVERT: A 262 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.4925 (mp0) REVERT: A 572 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: B 176 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7245 (mp) REVERT: B 214 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: B 221 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7564 (p0) outliers start: 34 outliers final: 24 residues processed: 119 average time/residue: 0.1071 time to fit residues: 17.5681 Evaluate side-chains 117 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 104 GLN A 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126637 restraints weight = 11126.134| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.89 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9561 Z= 0.141 Angle : 0.539 6.836 13168 Z= 0.292 Chirality : 0.041 0.149 1464 Planarity : 0.004 0.040 1526 Dihedral : 17.017 138.371 1786 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.14 % Favored : 92.76 % Rotamer: Outliers : 4.05 % Allowed : 28.49 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.76 (0.26), residues: 1036 helix: 1.26 (0.28), residues: 380 sheet: -0.39 (0.40), residues: 186 loop : -2.11 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 105 TYR 0.018 0.001 TYR A 74 PHE 0.017 0.001 PHE A 328 TRP 0.012 0.001 TRP B 377 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9561) covalent geometry : angle 0.53888 / 0.29 (13168) hydrogen bonds : bond 0.03706 / 2.41 ( 365) hydrogen bonds : angle 4.46250 / 3.04 ( 1046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.387 Fit side-chains REVERT: A 46 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.4915 (t70) REVERT: A 115 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6022 (ptm160) REVERT: A 260 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7551 (mmtp) REVERT: A 262 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5007 (mp0) REVERT: A 572 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: B 176 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7267 (mp) REVERT: B 214 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (mtpt) REVERT: B 221 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7327 (p0) outliers start: 36 outliers final: 23 residues processed: 117 average time/residue: 0.1046 time to fit residues: 16.8750 Evaluate side-chains 119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127585 restraints weight = 10921.180| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.98 r_work: 0.3077 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9561 Z= 0.112 Angle : 0.522 6.664 13168 Z= 0.284 Chirality : 0.040 0.147 1464 Planarity : 0.004 0.042 1526 Dihedral : 17.002 137.428 1786 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 3.38 % Allowed : 28.83 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.26), residues: 1036 helix: 1.30 (0.28), residues: 379 sheet: -0.41 (0.39), residues: 190 loop : -2.09 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 168 TYR 0.016 0.001 TYR A 74 PHE 0.016 0.001 PHE A 328 TRP 0.012 0.001 TRP B 377 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9561) covalent geometry : angle 0.52186 / 0.28 (13168) hydrogen bonds : bond 0.03536 / 2.29 ( 365) hydrogen bonds : angle 4.42737 / 3.01 ( 1046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2300.53 seconds wall clock time: 40 minutes 11.13 seconds (2411.13 seconds total)