Starting phenix.real_space_refine on Wed Sep 17 14:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8z_39064/09_2025/8y8z_39064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8z_39064/09_2025/8y8z_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_39064/09_2025/8y8z_39064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8z_39064/09_2025/8y8z_39064.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8z_39064/09_2025/8y8z_39064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8z_39064/09_2025/8y8z_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-2.0-5805/lib/python3.9/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, 23 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 2.47, per 1000 atoms: 0.27 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 215.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.18 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: 1.15 Time building geometry restraints manager: 0.87 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 2.470 nonbonded pdb=" OG SER E 318 " pdb="CL CL E 703 " model vdw 1.845 3.190 nonbonded pdb=" OH TYR E 98 " pdb="CL CL E 703 " model vdw 1.868 3.190 nonbonded pdb=" OH TYR A 98 " pdb="CL CL A 703 " model vdw 1.982 3.190 nonbonded pdb=" O VAL E 74 " pdb="NA NA E 702 " model vdw 2.177 2.470 ... (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: 2.090 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 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 aren 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 covalent geometry : bond 0.00696 ( 9374) covalent geometry : angle 0.62962 (12796) hydrogen bonds : bond 0.15517 ( 495) hydrogen bonds : angle 6.85474 ( 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 : 0.342 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: 0.5886 (mm) REVERT: E 386 LEU cc_start: 0.7592 (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: 0.0808 time to fit residues: 33.2617 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 : 0.280 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.200589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170481 restraints weight = 11524.360| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.20 r_work: 0.3888 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9374 Z= 0.149 Angle : 0.602 8.838 12796 Z= 0.307 Chirality : 0.041 0.171 1422 Planarity : 0.004 0.038 1556 Dihedral : 6.934 70.795 1286 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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 aren not related in a simple way. whole: -0.74 (0.25), residues: 1126 helix: 0.12 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.62 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 604 TYR 0.012 0.001 TYR E 151 PHE 0.023 0.002 PHE A 403 TRP 0.018 0.001 TRP E 585 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9374) covalent geometry : angle 0.60240 (12796) hydrogen bonds : bond 0.03526 ( 495) hydrogen bonds : angle 4.32465 ( 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 203 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.340 Fit side-chains REVERT: A 254 LYS cc_start: 0.8531 (mttm) cc_final: 0.8255 (mtmt) REVERT: E 63 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6346 (tp) REVERT: E 254 LYS cc_start: 0.8526 (mttm) cc_final: 0.8292 (mtmt) REVERT: E 368 MET cc_start: 0.6708 (tmm) cc_final: 0.6418 (tpp) REVERT: E 386 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7920 (tt) REVERT: E 481 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8048 (tp) REVERT: E 504 ASP cc_start: 0.6828 (m-30) cc_final: 0.6575 (m-30) outliers start: 42 outliers final: 23 residues processed: 192 average time/residue: 0.0775 time to fit residues: 22.3340 Evaluate side-chains 166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 70 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.206199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177458 restraints weight = 11499.508| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.12 r_work: 0.3954 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9374 Z= 0.114 Angle : 0.551 7.800 12796 Z= 0.279 Chirality : 0.039 0.167 1422 Planarity : 0.004 0.038 1556 Dihedral : 6.132 75.538 1275 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.52 % Allowed : 16.39 % Favored : 79.10 % 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 aren not related in a simple way. whole: -0.09 (0.25), 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 0.005 0.000 ARG A 216 TYR 0.018 0.001 TYR E 294 PHE 0.017 0.001 PHE A 317 TRP 0.018 0.001 TRP A 585 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9374) covalent geometry : angle 0.55140 (12796) hydrogen bonds : bond 0.03166 ( 495) hydrogen bonds : angle 4.03125 ( 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 193 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.339 Fit side-chains REVERT: A 133 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: A 230 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 254 LYS cc_start: 0.8524 (mttm) cc_final: 0.8309 (mtmt) REVERT: A 386 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 487 MET cc_start: 0.8463 (mmm) cc_final: 0.8003 (mmt) REVERT: E 63 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6338 (tp) REVERT: E 133 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8012 (m-10) REVERT: E 230 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7396 (mt) REVERT: E 481 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8051 (tp) REVERT: E 504 ASP cc_start: 0.6687 (m-30) cc_final: 0.6479 (m-30) outliers start: 43 outliers final: 27 residues processed: 180 average time/residue: 0.0801 time to fit residues: 21.7048 Evaluate side-chains 163 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 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 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: 0.2980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.199864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170213 restraints weight = 11800.478| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.16 r_work: 0.3912 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9374 Z= 0.154 Angle : 0.592 8.402 12796 Z= 0.299 Chirality : 0.040 0.177 1422 Planarity : 0.004 0.035 1556 Dihedral : 5.862 77.789 1269 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.36 % Allowed : 14.71 % Favored : 79.94 % 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 aren not related in a simple way. whole: -0.02 (0.25), residues: 1126 helix: 0.74 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.018 0.002 TYR E 294 PHE 0.015 0.001 PHE E 403 TRP 0.019 0.001 TRP A 585 HIS 0.003 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9374) covalent geometry : angle 0.59222 (12796) hydrogen bonds : bond 0.03422 ( 495) hydrogen bonds : angle 4.05185 ( 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 187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 0.363 Fit side-chains REVERT: A 230 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7648 (mt) REVERT: A 386 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7962 (tt) REVERT: E 230 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7817 (mt) REVERT: E 367 TYR cc_start: 0.6744 (t80) cc_final: 0.6494 (t80) REVERT: E 368 MET cc_start: 0.6780 (tmm) cc_final: 0.6339 (tpp) REVERT: E 481 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8145 (tp) outliers start: 51 outliers final: 31 residues processed: 173 average time/residue: 0.0821 time to fit residues: 21.1047 Evaluate side-chains 155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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 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 418 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.203446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.174344 restraints weight = 11609.276| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.13 r_work: 0.3953 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9374 Z= 0.110 Angle : 0.543 9.068 12796 Z= 0.272 Chirality : 0.038 0.178 1422 Planarity : 0.004 0.037 1556 Dihedral : 5.724 82.144 1269 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.99 % Allowed : 17.12 % Favored : 78.89 % 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 aren not related in a simple way. whole: 0.32 (0.25), residues: 1126 helix: 1.07 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.023 0.001 TYR E 294 PHE 0.016 0.001 PHE E 316 TRP 0.020 0.001 TRP A 585 HIS 0.003 0.000 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9374) covalent geometry : angle 0.54310 (12796) hydrogen bonds : bond 0.02959 ( 495) hydrogen bonds : angle 3.90441 ( 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 175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.330 Fit side-chains REVERT: A 230 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 386 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 487 MET cc_start: 0.8576 (mmm) cc_final: 0.8267 (mmt) REVERT: E 63 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6251 (tp) REVERT: E 230 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7401 (mt) REVERT: E 481 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8095 (tp) outliers start: 38 outliers final: 28 residues processed: 167 average time/residue: 0.0703 time to fit residues: 18.4987 Evaluate side-chains 154 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 349 ILE 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 600 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 63 ILE 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 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: 2.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 55 optimal weight: 0.0010 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.205205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.176247 restraints weight = 11600.742| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.14 r_work: 0.3970 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9374 Z= 0.106 Angle : 0.555 9.423 12796 Z= 0.272 Chirality : 0.038 0.183 1422 Planarity : 0.004 0.037 1556 Dihedral : 5.747 88.308 1269 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.41 % Allowed : 18.07 % 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 aren not related in a simple way. whole: 0.63 (0.26), residues: 1126 helix: 1.30 (0.20), residues: 744 sheet: None (None), residues: 0 loop : -1.35 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.019 0.001 TYR E 294 PHE 0.026 0.001 PHE E 403 TRP 0.021 0.001 TRP A 585 HIS 0.007 0.001 HIS E 599 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9374) covalent geometry : angle 0.55478 (12796) hydrogen bonds : bond 0.02894 ( 495) hydrogen bonds : angle 3.86946 ( 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 167 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.349 Fit side-chains REVERT: A 230 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 386 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (tt) REVERT: E 63 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6182 (tp) REVERT: E 128 TRP cc_start: 0.8379 (m100) cc_final: 0.8168 (m100) REVERT: E 230 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7492 (mt) REVERT: E 332 TYR cc_start: 0.7467 (m-10) cc_final: 0.7077 (m-10) REVERT: E 368 MET cc_start: 0.6930 (tmm) cc_final: 0.6353 (tpp) REVERT: E 481 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8073 (tp) REVERT: E 504 ASP cc_start: 0.6752 (m-30) cc_final: 0.6491 (m-30) outliers start: 42 outliers final: 29 residues processed: 157 average time/residue: 0.0669 time to fit residues: 16.7047 Evaluate side-chains 158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 529 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 63 ILE 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 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 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.200404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.170960 restraints weight = 11705.281| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.15 r_work: 0.3923 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9374 Z= 0.135 Angle : 0.577 9.228 12796 Z= 0.286 Chirality : 0.039 0.191 1422 Planarity : 0.004 0.037 1556 Dihedral : 5.615 72.977 1269 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.41 % Allowed : 18.17 % Favored : 77.42 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 1126 helix: 1.32 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.018 0.002 TYR E 294 PHE 0.014 0.001 PHE E 362 TRP 0.019 0.001 TRP E 585 HIS 0.003 0.001 HIS E 599 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9374) covalent geometry : angle 0.57687 (12796) hydrogen bonds : bond 0.03195 ( 495) hydrogen bonds : angle 3.95479 ( 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 175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.384 Fit side-chains REVERT: A 230 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 386 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7937 (tt) REVERT: A 518 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7296 (mtm110) REVERT: E 63 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6179 (tp) REVERT: E 230 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7621 (mt) REVERT: E 242 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5796 (ttt) REVERT: E 481 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8150 (tp) outliers start: 42 outliers final: 30 residues processed: 164 average time/residue: 0.0732 time to fit residues: 18.4652 Evaluate side-chains 158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 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 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 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 529 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 127 VAL 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 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.205623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176966 restraints weight = 11634.503| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.11 r_work: 0.3990 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 9374 Z= 0.103 Angle : 0.548 9.665 12796 Z= 0.270 Chirality : 0.038 0.189 1422 Planarity : 0.004 0.038 1556 Dihedral : 5.110 53.098 1269 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.20 % Allowed : 18.80 % Favored : 77.00 % 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 aren not related in a simple way. whole: 0.90 (0.26), residues: 1126 helix: 1.55 (0.20), residues: 736 sheet: None (None), residues: 0 loop : -1.28 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 587 TYR 0.021 0.001 TYR E 294 PHE 0.027 0.001 PHE E 403 TRP 0.022 0.001 TRP A 585 HIS 0.002 0.000 HIS E 599 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9374) covalent geometry : angle 0.54809 (12796) hydrogen bonds : bond 0.02838 ( 495) hydrogen bonds : angle 3.88409 ( 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 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.337 Fit side-chains REVERT: A 63 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6062 (tp) REVERT: A 230 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (mt) REVERT: A 332 TYR cc_start: 0.7598 (m-10) cc_final: 0.7262 (m-10) REVERT: A 386 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 508 MET cc_start: 0.8034 (ttm) cc_final: 0.7705 (ttm) REVERT: A 518 ARG cc_start: 0.7595 (mtm180) cc_final: 0.7317 (mtm110) REVERT: E 63 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6106 (tp) REVERT: E 230 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7489 (mt) REVERT: E 332 TYR cc_start: 0.7424 (m-10) cc_final: 0.7089 (m-10) REVERT: E 481 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8081 (tp) outliers start: 40 outliers final: 28 residues processed: 169 average time/residue: 0.0728 time to fit residues: 19.0056 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU 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 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 600 LEU Chi-restraints excluded: chain E residue 63 ILE 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 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 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 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: 0.7980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.203198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174234 restraints weight = 11658.341| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.14 r_work: 0.3900 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9374 Z= 0.116 Angle : 0.565 12.023 12796 Z= 0.277 Chirality : 0.038 0.192 1422 Planarity : 0.004 0.037 1556 Dihedral : 4.857 35.929 1269 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.10 % Allowed : 19.22 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1126 helix: 1.50 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.019 0.002 TYR E 294 PHE 0.026 0.001 PHE E 403 TRP 0.021 0.001 TRP E 585 HIS 0.002 0.000 HIS E 599 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9374) covalent geometry : angle 0.56530 (12796) hydrogen bonds : bond 0.02970 ( 495) hydrogen bonds : angle 3.88697 ( 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 168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.342 Fit side-chains REVERT: A 63 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6063 (tp) REVERT: A 230 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 332 TYR cc_start: 0.7623 (m-10) cc_final: 0.7233 (m-10) REVERT: A 386 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7831 (tt) REVERT: A 508 MET cc_start: 0.8095 (ttm) cc_final: 0.7716 (ttm) REVERT: E 63 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6148 (tp) REVERT: E 133 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: E 230 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7497 (mt) REVERT: E 332 TYR cc_start: 0.7446 (m-10) cc_final: 0.7116 (m-10) REVERT: E 481 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8108 (tp) REVERT: E 487 MET cc_start: 0.8468 (mmm) cc_final: 0.8127 (mmt) outliers start: 39 outliers final: 30 residues processed: 159 average time/residue: 0.0689 time to fit residues: 17.3058 Evaluate side-chains 162 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU 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 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 529 LEU Chi-restraints excluded: chain E residue 63 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 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 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 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 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: 2.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.204062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175302 restraints weight = 11666.599| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.13 r_work: 0.3961 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 9374 Z= 0.122 Angle : 0.592 11.777 12796 Z= 0.291 Chirality : 0.039 0.200 1422 Planarity : 0.004 0.037 1556 Dihedral : 4.840 35.804 1269 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.99 % Allowed : 19.64 % Favored : 76.37 % 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 aren not related in a simple way. whole: 0.77 (0.26), residues: 1126 helix: 1.49 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.51 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.018 0.001 TYR E 294 PHE 0.027 0.001 PHE E 403 TRP 0.023 0.001 TRP A 585 HIS 0.002 0.000 HIS E 599 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9374) covalent geometry : angle 0.59208 (12796) hydrogen bonds : bond 0.03035 ( 495) hydrogen bonds : angle 3.95089 ( 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 161 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.254 Fit side-chains REVERT: A 63 ILE cc_start: 0.6509 (OUTLIER) cc_final: 0.6049 (tp) REVERT: A 230 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (mt) REVERT: A 332 TYR cc_start: 0.7642 (m-10) cc_final: 0.7219 (m-10) REVERT: A 386 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 487 MET cc_start: 0.8595 (mmm) cc_final: 0.8151 (mmt) REVERT: E 63 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6152 (tp) REVERT: E 133 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: E 230 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7633 (mt) REVERT: E 481 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8126 (tp) REVERT: E 487 MET cc_start: 0.8475 (mmm) cc_final: 0.8138 (mmt) outliers start: 38 outliers final: 30 residues processed: 152 average time/residue: 0.0602 time to fit residues: 14.4595 Evaluate side-chains 156 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE 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 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 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 529 LEU Chi-restraints excluded: chain E residue 63 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 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 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 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 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: 0.8980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 22 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.202257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.173356 restraints weight = 11548.282| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.15 r_work: 0.3951 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9374 Z= 0.124 Angle : 0.590 11.262 12796 Z= 0.290 Chirality : 0.039 0.201 1422 Planarity : 0.004 0.037 1556 Dihedral : 4.836 35.615 1269 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.99 % Allowed : 19.75 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1126 helix: 1.45 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.51 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 121 TYR 0.020 0.001 TYR A 119 PHE 0.026 0.001 PHE E 403 TRP 0.022 0.001 TRP A 585 HIS 0.002 0.000 HIS E 599 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9374) covalent geometry : angle 0.58957 (12796) hydrogen bonds : bond 0.03082 ( 495) hydrogen bonds : angle 3.95707 ( 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: 2024.67 seconds wall clock time: 35 minutes 10.73 seconds (2110.73 seconds total)