Starting phenix.real_space_refine on Thu Jul 2 14:46:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8z_39064/07_2026/8y8z_39064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8z_39064/07_2026/8y8z_39064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8z_39064/07_2026/8y8z_39064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8z_39064/07_2026/8y8z_39064.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8z_39064/07_2026/8y8z_39064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8z_39064/07_2026/8y8z_39064.cif" } resolution = 3.29 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= 0.001 sd= 0.047 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 6092 2.51 5 N 1414 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 9082 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "E" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'A1LX3': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'A1LX3': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.71, per 1000 atoms: 0.19 Number of scatterers: 9082 At special positions: 0 Unit cell: (97.09, 113.15, 91.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 40 16.00 Na 2 11.00 O 1532 8.00 N 1414 7.00 C 6092 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: 0.69 Conformation dependent library (CDL) restraints added in 218.7 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 0 sheets defined 74.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 4.112A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 91 through 104 removed outlier: 4.250A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.716A pdb=" N VAL A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 128' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.732A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.584A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.717A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 244 " --> pdb=" O CYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.734A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 4.289A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 308 through 320 removed outlier: 4.037A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 removed outlier: 3.587A pdb=" N ILE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 373 removed outlier: 3.608A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.248A pdb=" N GLU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.676A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.372A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.998A pdb=" N ALA A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.874A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.969A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.765A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.951A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 603' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.147A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 removed outlier: 3.916A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.503A pdb=" N VAL E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 91 through 104 removed outlier: 4.182A pdb=" N ILE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Proline residue: E 97 - end of helix Processing helix chain 'E' and resid 106 through 120 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.624A pdb=" N VAL E 127 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP E 128 " --> pdb=" O ALA E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 134 through 166 removed outlier: 3.677A pdb=" N GLY E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 162 " --> pdb=" O TRP E 158 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.612A pdb=" N GLU E 223 " --> pdb=" O HIS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.676A pdb=" N CYS E 240 " --> pdb=" O GLN E 236 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 244 " --> pdb=" O CYS E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.820A pdb=" N SER E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 4.248A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR E 283 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 306 through 320 removed outlier: 4.978A pdb=" N ALA E 312 " --> pdb=" O TRP E 308 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 314 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.544A pdb=" N ILE E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 373 removed outlier: 3.591A pdb=" N SER E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 380 removed outlier: 3.510A pdb=" N ALA E 380 " --> pdb=" O ILE E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 398 removed outlier: 4.272A pdb=" N GLU E 393 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 432 removed outlier: 3.650A pdb=" N TRP E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 431 " --> pdb=" O VAL E 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 441 removed outlier: 4.298A pdb=" N ARG E 440 " --> pdb=" O GLN E 436 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS E 441 " --> pdb=" O VAL E 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 436 through 441' Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 471 through 476 removed outlier: 3.501A pdb=" N PHE E 475 " --> pdb=" O LEU E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 494 removed outlier: 3.687A pdb=" N VAL E 485 " --> pdb=" O ILE E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 509 Processing helix chain 'E' and resid 514 through 523 removed outlier: 3.886A pdb=" N LYS E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 539 Processing helix chain 'E' and resid 551 through 567 removed outlier: 3.991A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP E 556 " --> pdb=" O PRO E 552 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 579 Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.839A pdb=" N LEU E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 598 through 603 removed outlier: 4.104A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN E 603 " --> pdb=" O HIS E 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 598 through 603' Processing helix chain 'E' and resid 610 through 615 removed outlier: 4.130A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1467 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: 1.56 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2708 1.36 - 1.49: 2824 1.49 - 1.62: 3778 1.62 - 1.75: 0 1.75 - 1.88: 64 Bond restraints: 9374 Sorted by residual: bond pdb=" C07 A1LX3 A 701 " pdb=" C08 A1LX3 A 701 " ideal model delta sigma weight residual 1.539 1.884 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C07 A1LX3 E 701 " pdb=" C08 A1LX3 E 701 " ideal model delta sigma weight residual 1.539 1.874 -0.335 2.00e-02 2.50e+03 2.81e+02 bond pdb=" C16 A1LX3 E 701 " pdb=" C21 A1LX3 E 701 " ideal model delta sigma weight residual 1.399 1.257 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C16 A1LX3 A 701 " pdb=" C21 A1LX3 A 701 " ideal model delta sigma weight residual 1.399 1.268 0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C12 A1LX3 E 701 " pdb=" C13 A1LX3 E 701 " ideal model delta sigma weight residual 1.387 1.261 0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12543 1.85 - 3.70: 201 3.70 - 5.55: 40 5.55 - 7.40: 7 7.40 - 9.25: 5 Bond angle restraints: 12796 Sorted by residual: angle pdb=" N VAL E 468 " pdb=" CA VAL E 468 " pdb=" C VAL E 468 " ideal model delta sigma weight residual 112.43 107.98 4.45 9.20e-01 1.18e+00 2.34e+01 angle pdb=" N VAL A 468 " pdb=" CA VAL A 468 " pdb=" C VAL A 468 " ideal model delta sigma weight residual 112.17 107.94 4.23 9.50e-01 1.11e+00 1.98e+01 angle pdb=" N VAL A 127 " pdb=" CA VAL A 127 " pdb=" C VAL A 127 " ideal model delta sigma weight residual 113.07 108.15 4.92 1.37e+00 5.33e-01 1.29e+01 angle pdb=" N VAL E 127 " pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 113.07 108.20 4.87 1.37e+00 5.33e-01 1.26e+01 angle pdb=" C06 A1LX3 E 701 " pdb=" C07 A1LX3 E 701 " pdb=" C08 A1LX3 E 701 " ideal model delta sigma weight residual 111.38 102.13 9.25 3.00e+00 1.11e-01 9.50e+00 ... (remaining 12791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4926 17.32 - 34.63: 254 34.63 - 51.95: 66 51.95 - 69.26: 12 69.26 - 86.58: 4 Dihedral angle restraints: 5262 sinusoidal: 1998 harmonic: 3264 Sorted by residual: dihedral pdb=" CA ALA E 305 " pdb=" C ALA E 305 " pdb=" N THR E 306 " pdb=" CA THR E 306 " ideal model delta harmonic sigma weight residual 180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR E 179 " pdb=" C THR E 179 " pdb=" N TRP E 180 " pdb=" CA TRP E 180 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N TRP A 180 " pdb=" CA TRP A 180 " ideal model delta harmonic sigma weight residual -180.00 -164.33 -15.67 0 5.00e+00 4.00e-02 9.82e+00 ... (remaining 5259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1264 0.055 - 0.110: 155 0.110 - 0.166: 1 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" C06 A1LX3 E 701 " pdb=" C07 A1LX3 E 701 " pdb=" C15 A1LX3 E 701 " pdb=" C21 A1LX3 E 701 " both_signs ideal model delta sigma weight residual False 3.11 2.84 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C06 A1LX3 A 701 " pdb=" C07 A1LX3 A 701 " pdb=" C15 A1LX3 A 701 " pdb=" C21 A1LX3 A 701 " both_signs ideal model delta sigma weight residual False 3.11 2.87 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE E 549 " pdb=" N ILE E 549 " pdb=" C ILE E 549 " pdb=" CB ILE E 549 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 1419 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 54 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 55 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 54 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 55 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 525 " 0.019 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO E 526 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 526 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 526 " 0.016 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 31 2.39 - 3.02: 5145 3.02 - 3.64: 14176 3.64 - 4.27: 21382 4.27 - 4.90: 35510 Nonbonded interactions: 76244 Sorted by model distance: nonbonded pdb=" O GLY E 71 " pdb="NA NA E 702 " model vdw 1.761 3.210 nonbonded pdb=" OG SER E 318 " pdb="CL CL E 703 " model vdw 1.845 3.270 nonbonded pdb=" OH TYR E 98 " pdb="CL CL E 703 " model vdw 1.868 3.270 nonbonded pdb=" OH TYR A 98 " pdb="CL CL A 703 " model vdw 1.982 3.270 nonbonded pdb=" O VAL E 74 " pdb="NA NA E 702 " model vdw 2.177 3.210 ... (remaining 76239 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } 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: 2.960 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.950 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 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 : 0.007 0.345 9374 Z= 0.355 Angle : 0.630 9.247 12796 Z= 0.361 Chirality : 0.036 0.276 1422 Planarity : 0.003 0.037 1556 Dihedral : 11.548 86.575 3186 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.41 % Allowed : 8.93 % Favored : 84.66 % 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: -2.01 (0.23), residues: 1126 helix: -1.02 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -1.70 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.010 0.001 TYR A 151 PHE 0.008 0.001 PHE E 362 TRP 0.003 0.001 TRP E 308 HIS 0.001 0.000 HIS E 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.36 ( 9374) covalent geometry : angle 0.62962 / 0.36 (12796) hydrogen bonds : bond 0.15517 / 10.41 ( 495) hydrogen bonds : angle 6.85474 / 4.68 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8477 (mttm) cc_final: 0.8035 (mtmt) REVERT: A 386 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6924 (tt) REVERT: A 389 ILE cc_start: 0.8099 (mm) cc_final: 0.7815 (mm) REVERT: A 600 LEU cc_start: 0.8499 (mt) cc_final: 0.8194 (mt) REVERT: E 191 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6437 (mt) REVERT: E 349 ILE cc_start: 0.6118 (mt) cc_final: 0.5885 (mm) REVERT: E 386 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7347 (tt) REVERT: E 389 ILE cc_start: 0.8076 (mm) cc_final: 0.7856 (mm) outliers start: 61 outliers final: 9 residues processed: 283 average time/residue: 0.0802 time to fit residues: 33.3214 Evaluate side-chains 168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 462 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.200466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.170530 restraints weight = 11553.065| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.19 r_work: 0.3884 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9374 Z= 0.150 Angle : 0.608 8.864 12796 Z= 0.309 Chirality : 0.041 0.175 1422 Planarity : 0.004 0.038 1556 Dihedral : 6.928 70.204 1286 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.41 % Allowed : 14.71 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1126 helix: 0.14 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.63 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.012 0.001 TYR E 151 PHE 0.023 0.002 PHE A 403 TRP 0.017 0.001 TRP A 585 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9374) covalent geometry : angle 0.60771 / 0.31 (12796) hydrogen bonds : bond 0.03540 / 2.20 ( 495) hydrogen bonds : angle 4.33180 / 2.98 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.336 Fit side-chains REVERT: A 254 LYS cc_start: 0.8535 (mttm) cc_final: 0.8255 (mtmt) REVERT: E 63 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6304 (tp) REVERT: E 254 LYS cc_start: 0.8530 (mttm) cc_final: 0.8296 (mtmt) REVERT: E 368 MET cc_start: 0.6578 (tmm) cc_final: 0.6351 (tpp) REVERT: E 386 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7917 (tt) REVERT: E 481 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8047 (tp) REVERT: E 504 ASP cc_start: 0.6837 (m-30) cc_final: 0.6585 (m-30) outliers start: 42 outliers final: 23 residues processed: 191 average time/residue: 0.0770 time to fit residues: 22.1590 Evaluate side-chains 165 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.206050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.177360 restraints weight = 11498.391| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.10 r_work: 0.3951 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9374 Z= 0.119 Angle : 0.557 7.968 12796 Z= 0.281 Chirality : 0.039 0.168 1422 Planarity : 0.004 0.038 1556 Dihedral : 6.139 74.513 1275 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.73 % Allowed : 15.86 % Favored : 79.41 % 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: -0.09 (0.26), residues: 1126 helix: 0.70 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 604 TYR 0.016 0.001 TYR E 294 PHE 0.017 0.001 PHE A 317 TRP 0.018 0.001 TRP A 585 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9374) covalent geometry : angle 0.55700 / 0.28 (12796) hydrogen bonds : bond 0.03183 / 1.98 ( 495) hydrogen bonds : angle 4.04315 / 2.79 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.342 Fit side-chains REVERT: A 133 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8034 (m-10) REVERT: A 230 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 254 LYS cc_start: 0.8526 (mttm) cc_final: 0.8309 (mtmt) REVERT: A 386 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 487 MET cc_start: 0.8481 (mmm) cc_final: 0.8023 (mmt) REVERT: E 63 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6320 (tp) REVERT: E 133 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8018 (m-10) REVERT: E 230 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7464 (mt) REVERT: E 481 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8067 (tp) REVERT: E 504 ASP cc_start: 0.6712 (m-30) cc_final: 0.6504 (m-30) outliers start: 45 outliers final: 30 residues processed: 185 average time/residue: 0.0810 time to fit residues: 22.3953 Evaluate side-chains 168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.193185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161999 restraints weight = 11705.040| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.24 r_work: 0.3790 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9374 Z= 0.174 Angle : 0.614 8.549 12796 Z= 0.312 Chirality : 0.041 0.180 1422 Planarity : 0.004 0.036 1556 Dihedral : 6.076 76.222 1271 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.46 % Allowed : 14.92 % Favored : 79.62 % 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: -0.05 (0.25), residues: 1126 helix: 0.76 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -1.57 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.019 0.002 TYR E 294 PHE 0.022 0.002 PHE A 403 TRP 0.019 0.001 TRP A 585 HIS 0.003 0.001 HIS E 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 9374) covalent geometry : angle 0.61366 / 0.31 (12796) hydrogen bonds : bond 0.03613 / 2.24 ( 495) hydrogen bonds : angle 4.13290 / 2.86 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.268 Fit side-chains REVERT: A 230 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7591 (mt) REVERT: A 386 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7880 (tt) REVERT: E 242 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5914 (ttt) REVERT: E 367 TYR cc_start: 0.6791 (t80) cc_final: 0.6541 (t80) REVERT: E 368 MET cc_start: 0.6756 (tmm) cc_final: 0.6303 (tpp) REVERT: E 481 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8176 (tp) outliers start: 52 outliers final: 33 residues processed: 171 average time/residue: 0.0763 time to fit residues: 19.7581 Evaluate side-chains 158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 351 CYS Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.187772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.156174 restraints weight = 11603.886| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.29 r_work: 0.3743 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9374 Z= 0.184 Angle : 0.620 8.858 12796 Z= 0.315 Chirality : 0.041 0.181 1422 Planarity : 0.004 0.036 1556 Dihedral : 6.083 78.231 1269 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.25 % Allowed : 16.28 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1126 helix: 0.81 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.021 0.002 TYR E 294 PHE 0.018 0.002 PHE A 409 TRP 0.020 0.001 TRP A 585 HIS 0.003 0.001 HIS E 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 9374) covalent geometry : angle 0.62002 / 0.32 (12796) hydrogen bonds : bond 0.03712 / 2.29 ( 495) hydrogen bonds : angle 4.20517 / 2.91 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.340 Fit side-chains REVERT: A 230 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 386 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7888 (tt) REVERT: E 242 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5957 (ttt) REVERT: E 367 TYR cc_start: 0.6760 (t80) cc_final: 0.6555 (t80) REVERT: E 408 PHE cc_start: 0.8533 (t80) cc_final: 0.8267 (t80) REVERT: E 481 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8225 (tp) outliers start: 50 outliers final: 34 residues processed: 173 average time/residue: 0.0771 time to fit residues: 20.3370 Evaluate side-chains 160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 351 CYS Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.191169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.160431 restraints weight = 11457.487| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.22 r_work: 0.3792 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9374 Z= 0.131 Angle : 0.577 9.086 12796 Z= 0.289 Chirality : 0.039 0.172 1422 Planarity : 0.004 0.037 1556 Dihedral : 5.989 82.775 1269 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.62 % Allowed : 17.23 % Favored : 78.15 % 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: 0.30 (0.25), residues: 1126 helix: 1.10 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.021 0.001 TYR A 294 PHE 0.016 0.001 PHE A 403 TRP 0.013 0.001 TRP A 585 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9374) covalent geometry : angle 0.57731 / 0.29 (12796) hydrogen bonds : bond 0.03307 / 2.03 ( 495) hydrogen bonds : angle 4.07789 / 2.81 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.314 Fit side-chains REVERT: A 230 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7671 (mt) REVERT: A 386 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7811 (tt) REVERT: A 487 MET cc_start: 0.8657 (mmm) cc_final: 0.8383 (mmt) REVERT: E 63 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.6107 (tp) REVERT: E 242 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5892 (ttt) REVERT: E 332 TYR cc_start: 0.7528 (m-10) cc_final: 0.7081 (m-10) REVERT: E 368 MET cc_start: 0.6978 (tmm) cc_final: 0.6403 (tpp) REVERT: E 481 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8261 (tp) REVERT: E 586 GLU cc_start: 0.8090 (tt0) cc_final: 0.7876 (tp30) outliers start: 44 outliers final: 31 residues processed: 163 average time/residue: 0.0755 time to fit residues: 18.8175 Evaluate side-chains 157 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.197956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167851 restraints weight = 11486.673| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.20 r_work: 0.3856 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 9374 Z= 0.106 Angle : 0.545 9.302 12796 Z= 0.271 Chirality : 0.037 0.174 1422 Planarity : 0.004 0.039 1556 Dihedral : 5.789 85.407 1269 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.68 % Allowed : 18.80 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1126 helix: 1.49 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -1.35 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.020 0.001 TYR E 294 PHE 0.021 0.001 PHE E 72 TRP 0.022 0.001 TRP A 585 HIS 0.004 0.000 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9374) covalent geometry : angle 0.54538 / 0.27 (12796) hydrogen bonds : bond 0.02917 / 1.78 ( 495) hydrogen bonds : angle 3.93893 / 2.71 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.240 Fit side-chains REVERT: A 189 LYS cc_start: 0.6358 (mmmt) cc_final: 0.6071 (ptpt) REVERT: A 386 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 506 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: A 508 MET cc_start: 0.8034 (ttm) cc_final: 0.7820 (ttm) REVERT: A 586 GLU cc_start: 0.8348 (tt0) cc_final: 0.8064 (tp30) REVERT: E 63 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.6008 (tp) REVERT: E 332 TYR cc_start: 0.7289 (m-10) cc_final: 0.7063 (m-10) REVERT: E 481 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8265 (tp) outliers start: 35 outliers final: 24 residues processed: 166 average time/residue: 0.0645 time to fit residues: 16.5107 Evaluate side-chains 151 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.166947 restraints weight = 11544.174| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.20 r_work: 0.3853 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9374 Z= 0.117 Angle : 0.572 9.644 12796 Z= 0.281 Chirality : 0.038 0.178 1422 Planarity : 0.004 0.038 1556 Dihedral : 5.546 68.484 1269 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.57 % Allowed : 19.54 % Favored : 76.89 % 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: 0.91 (0.26), residues: 1126 helix: 1.62 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -1.31 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.019 0.001 TYR E 294 PHE 0.026 0.001 PHE E 403 TRP 0.023 0.001 TRP E 585 HIS 0.003 0.000 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9374) covalent geometry : angle 0.57150 / 0.28 (12796) hydrogen bonds : bond 0.03012 / 1.84 ( 495) hydrogen bonds : angle 3.91785 / 2.70 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.342 Fit side-chains REVERT: A 189 LYS cc_start: 0.6398 (mmmt) cc_final: 0.6134 (ptpt) REVERT: A 386 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7721 (tt) REVERT: A 506 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: A 508 MET cc_start: 0.8077 (ttm) cc_final: 0.7798 (ttm) REVERT: A 586 GLU cc_start: 0.8364 (tt0) cc_final: 0.8133 (tp30) REVERT: E 63 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6100 (tp) REVERT: E 230 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7556 (mt) REVERT: E 332 TYR cc_start: 0.7339 (m-10) cc_final: 0.7069 (m-10) REVERT: E 403 PHE cc_start: 0.8266 (t80) cc_final: 0.7974 (t80) REVERT: E 481 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8287 (tp) REVERT: E 504 ASP cc_start: 0.6760 (m-30) cc_final: 0.6460 (m-30) REVERT: E 508 MET cc_start: 0.7804 (ttm) cc_final: 0.7444 (mtt) outliers start: 34 outliers final: 27 residues processed: 152 average time/residue: 0.0716 time to fit residues: 17.0779 Evaluate side-chains 152 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.196523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166445 restraints weight = 11497.923| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.18 r_work: 0.3842 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9374 Z= 0.122 Angle : 0.580 11.713 12796 Z= 0.284 Chirality : 0.039 0.178 1422 Planarity : 0.004 0.038 1556 Dihedral : 5.084 40.873 1269 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.57 % Allowed : 19.54 % Favored : 76.89 % 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: 0.97 (0.26), residues: 1126 helix: 1.64 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -1.25 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.018 0.001 TYR E 294 PHE 0.026 0.001 PHE E 403 TRP 0.017 0.001 TRP E 585 HIS 0.006 0.001 HIS E 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9374) covalent geometry : angle 0.58043 / 0.28 (12796) hydrogen bonds : bond 0.03028 / 1.86 ( 495) hydrogen bonds : angle 3.93616 / 2.71 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.286 Fit side-chains REVERT: A 386 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7726 (tt) REVERT: A 487 MET cc_start: 0.8630 (mmm) cc_final: 0.8323 (mmt) REVERT: A 506 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: A 508 MET cc_start: 0.8074 (ttm) cc_final: 0.7682 (ttm) REVERT: A 586 GLU cc_start: 0.8378 (tt0) cc_final: 0.8153 (tp30) REVERT: E 63 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.6088 (tp) REVERT: E 230 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7542 (mt) REVERT: E 332 TYR cc_start: 0.7374 (m-10) cc_final: 0.7013 (m-10) REVERT: E 403 PHE cc_start: 0.8317 (t80) cc_final: 0.8087 (t80) REVERT: E 481 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8299 (tp) REVERT: E 487 MET cc_start: 0.8562 (mmm) cc_final: 0.8211 (mmt) REVERT: E 504 ASP cc_start: 0.6844 (m-30) cc_final: 0.6591 (m-30) REVERT: E 508 MET cc_start: 0.7857 (ttm) cc_final: 0.7515 (mtt) outliers start: 34 outliers final: 26 residues processed: 147 average time/residue: 0.0656 time to fit residues: 15.3036 Evaluate side-chains 150 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 94 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.197927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.168063 restraints weight = 11429.787| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.16 r_work: 0.3868 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9374 Z= 0.113 Angle : 0.568 10.847 12796 Z= 0.278 Chirality : 0.038 0.182 1422 Planarity : 0.004 0.039 1556 Dihedral : 4.852 35.590 1269 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.36 % Allowed : 19.85 % Favored : 76.79 % 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: 1.04 (0.26), residues: 1126 helix: 1.67 (0.20), residues: 730 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.019 0.001 TYR A 119 PHE 0.025 0.001 PHE E 403 TRP 0.017 0.001 TRP E 585 HIS 0.006 0.001 HIS E 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9374) covalent geometry : angle 0.56803 / 0.28 (12796) hydrogen bonds : bond 0.02910 / 1.78 ( 495) hydrogen bonds : angle 3.89256 / 2.68 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.331 Fit side-chains REVERT: A 386 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 506 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: E 63 ILE cc_start: 0.6337 (OUTLIER) cc_final: 0.6064 (tp) REVERT: E 332 TYR cc_start: 0.7272 (m-10) cc_final: 0.7002 (m-10) REVERT: E 481 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8289 (tp) REVERT: E 487 MET cc_start: 0.8520 (mmm) cc_final: 0.8146 (mmt) REVERT: E 504 ASP cc_start: 0.6912 (m-30) cc_final: 0.6628 (m-30) REVERT: E 508 MET cc_start: 0.7725 (ttm) cc_final: 0.7367 (mtt) outliers start: 32 outliers final: 25 residues processed: 148 average time/residue: 0.0655 time to fit residues: 15.4215 Evaluate side-chains 149 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.186760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156015 restraints weight = 11581.691| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.18 r_work: 0.3731 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9374 Z= 0.249 Angle : 0.717 10.555 12796 Z= 0.358 Chirality : 0.044 0.182 1422 Planarity : 0.004 0.038 1556 Dihedral : 5.557 45.704 1269 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.10 % Allowed : 19.01 % Favored : 76.89 % 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: 0.23 (0.25), residues: 1126 helix: 1.07 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 216 TYR 0.031 0.002 TYR A 119 PHE 0.025 0.002 PHE E 403 TRP 0.018 0.002 TRP E 128 HIS 0.005 0.001 HIS E 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 ( 9374) covalent geometry : angle 0.71736 / 0.36 (12796) hydrogen bonds : bond 0.04164 / 2.58 ( 495) hydrogen bonds : angle 4.39649 / 3.05 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2068.88 seconds wall clock time: 36 minutes 5.35 seconds (2165.35 seconds total)