Starting phenix.real_space_refine on Sat Sep 12 04:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2026/6xlh_22244.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 5 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 8696 2.51 5 N 2240 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "C" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2544 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.01, per 1000 atoms: 0.22 Number of scatterers: 13608 At special positions: 0 Unit cell: (104.394, 113.436, 132.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 26 16.00 P 5 15.00 Mg 2 11.99 O 2637 8.00 N 2240 7.00 C 8696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 613.7 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 40.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.457A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 50 removed outlier: 4.083A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 85 through 92 removed outlier: 3.695A pdb=" N ILE A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.642A pdb=" N SER A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.825A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.578A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.569A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.678A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.590A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.566A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 4.372A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 removed outlier: 4.456A pdb=" N TYR A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 510 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.523A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.965A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.787A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 50 removed outlier: 4.143A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.659A pdb=" N GLU B 57 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.717A pdb=" N ILE B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.780A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.528A pdb=" N SER B 126 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.755A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.763A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.628A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 406 removed outlier: 3.908A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.603A pdb=" N ASP B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.622A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.652A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.509A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.427A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.952A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.580A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.664A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.789A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.675A pdb=" N TRP C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.569A pdb=" N SER C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.510A pdb=" N ILE C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 150 removed outlier: 3.827A pdb=" N GLY C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.619A pdb=" N ASN C 169 " --> pdb=" O TYR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.682A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 3.855A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.666A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.765A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.731A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 removed outlier: 3.955A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.682A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.523A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.599A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.102A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.727A pdb=" N ALA A 315 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 307 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.033A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.431A pdb=" N LYS A 560 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 611 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 562 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 7.286A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.890A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.550A pdb=" N LYS B 560 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 611 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 562 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.616A pdb=" N VAL C 12 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 58 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 34 removed outlier: 8.176A pdb=" N LYS C 43 " --> pdb=" O HIS C 78 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS C 78 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS C 45 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU C 76 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 74 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 77 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 213 through 218 removed outlier: 6.854A pdb=" N ILE C 216 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR C 318 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU C 218 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS C 316 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.706A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 218 removed outlier: 6.937A pdb=" N ILE D 216 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR D 318 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU D 218 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS D 316 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 274 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS D 284 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU D 272 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 286 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER D 270 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 596 hydrogen bonds defined for protein. 1650 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: 2.53 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4495 1.37 - 1.52: 4085 1.52 - 1.66: 5235 1.66 - 1.81: 42 1.81 - 1.95: 5 Bond restraints: 13862 Sorted by residual: bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.472 0.018 2.00e-02 2.50e+03 8.34e-01 bond pdb=" C ALA C 292 " pdb=" N PRO C 293 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.66e-01 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.245 1.235 0.010 1.41e-02 5.03e+03 5.11e-01 bond pdb=" C GLU B 655 " pdb=" N GLU B 656 " ideal model delta sigma weight residual 1.331 1.343 -0.012 2.07e-02 2.33e+03 3.60e-01 bond pdb=" N ILE C 320 " pdb=" CA ILE C 320 " ideal model delta sigma weight residual 1.461 1.468 -0.007 1.23e-02 6.61e+03 2.86e-01 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 18451 1.36 - 2.72: 187 2.72 - 4.08: 48 4.08 - 5.43: 17 5.43 - 6.79: 1 Bond angle restraints: 18704 Sorted by residual: angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" C VAL A 23 " ideal model delta sigma weight residual 113.71 108.38 5.33 9.50e-01 1.11e+00 3.15e+01 angle pdb=" N ILE B 384 " pdb=" CA ILE B 384 " pdb=" C ILE B 384 " ideal model delta sigma weight residual 113.53 108.18 5.35 9.80e-01 1.04e+00 2.98e+01 angle pdb=" N ILE A 384 " pdb=" CA ILE A 384 " pdb=" C ILE A 384 " ideal model delta sigma weight residual 113.53 108.69 4.84 9.80e-01 1.04e+00 2.44e+01 angle pdb=" CA ILE B 384 " pdb=" C ILE B 384 " pdb=" N MET B 385 " ideal model delta sigma weight residual 119.31 116.30 3.01 1.15e+00 7.56e-01 6.83e+00 angle pdb=" CA ILE A 384 " pdb=" C ILE A 384 " pdb=" N MET A 385 " ideal model delta sigma weight residual 119.31 116.51 2.80 1.15e+00 7.56e-01 5.94e+00 ... (remaining 18699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 8402 33.51 - 67.01: 30 67.01 - 100.52: 0 100.52 - 134.03: 2 134.03 - 167.53: 1 Dihedral angle restraints: 8435 sinusoidal: 3531 harmonic: 4904 Sorted by residual: dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 132.47 167.53 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sinusoidal sigma weight residual 68.91 -44.98 113.89 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 -173.26 105.53 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 8432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1362 0.030 - 0.059: 500 0.059 - 0.089: 102 0.089 - 0.118: 106 0.118 - 0.148: 17 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CA ILE C 154 " pdb=" N ILE C 154 " pdb=" C ILE C 154 " pdb=" CB ILE C 154 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C 320 " pdb=" N ILE C 320 " pdb=" C ILE C 320 " pdb=" CB ILE C 320 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2084 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 355 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO C 321 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.016 5.00e-02 4.00e+02 2.50e-02 9.99e-01 pdb=" N PRO B 355 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.014 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 320 2.70 - 3.31: 14840 3.31 - 3.92: 26511 3.92 - 4.53: 35564 4.53 - 5.14: 56834 Nonbonded interactions: 134069 Sorted by model distance: nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.134 2.170 nonbonded pdb=" OH TYR A 301 " pdb=" OE1 GLU A 402 " model vdw 2.253 3.040 nonbonded pdb=" O LYS A 480 " pdb=" OG1 THR B 658 " model vdw 2.256 3.040 ... (remaining 134064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 675 or resid 802 through 803)) selection = (chain 'B' and (resid 3 through 675 or resid 802 through 803)) } 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: 3.130 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.220 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.001 0.020 13862 Z= 0.067 Angle : 0.388 6.793 18704 Z= 0.223 Chirality : 0.039 0.148 2087 Planarity : 0.002 0.032 2388 Dihedral : 7.543 167.535 5243 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.13 % 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: -3.84 (0.16), residues: 1653 helix: -3.18 (0.12), residues: 613 sheet: -1.62 (0.25), residues: 362 loop : -2.23 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 322 TYR 0.008 0.000 TYR A 24 PHE 0.004 0.000 PHE A 609 TRP 0.005 0.001 TRP A 273 HIS 0.001 0.000 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00118 / 0.07 (13862) covalent geometry : angle 0.38769 / 0.22 (18704) hydrogen bonds : bond 0.26959 / 17.67 ( 582) hydrogen bonds : angle 8.36180 / 5.72 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7516 (mtpp) REVERT: C 301 THR cc_start: 0.8435 (m) cc_final: 0.8193 (m) REVERT: C 325 GLU cc_start: 0.7229 (pt0) cc_final: 0.6989 (pm20) outliers start: 2 outliers final: 0 residues processed: 475 average time/residue: 0.7193 time to fit residues: 367.8971 Evaluate side-chains 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN A 135 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN A 409 GLN A 592 GLN B 14 GLN B 26 ASN B 55 GLN B 91 ASN B 135 GLN B 335 ASN B 463 HIS C 4 ASN C 57 ASN C 94 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 306 GLN C 331 ASN D 207 GLN D 314 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113367 restraints weight = 21729.109| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.76 r_work: 0.3376 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13862 Z= 0.177 Angle : 0.600 6.867 18704 Z= 0.311 Chirality : 0.045 0.177 2087 Planarity : 0.004 0.044 2388 Dihedral : 6.760 157.143 1802 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.07 % Allowed : 15.07 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.90 (0.19), residues: 1653 helix: -0.77 (0.19), residues: 624 sheet: -1.35 (0.25), residues: 386 loop : -1.48 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 389 TYR 0.011 0.002 TYR C 23 PHE 0.016 0.002 PHE A 104 TRP 0.016 0.002 TRP A 581 HIS 0.005 0.002 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (13862) covalent geometry : angle 0.59982 / 0.31 (18704) hydrogen bonds : bond 0.04417 / 2.92 ( 582) hydrogen bonds : angle 5.45829 / 3.74 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 165 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: A 262 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7015 (mm-30) REVERT: A 339 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 384 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7958 (pt) REVERT: A 480 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8212 (mppt) REVERT: A 559 GLU cc_start: 0.7614 (tt0) cc_final: 0.6826 (mt-10) REVERT: B 543 TYR cc_start: 0.7881 (m-80) cc_final: 0.7642 (m-80) REVERT: B 559 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: C 78 HIS cc_start: 0.5988 (p-80) cc_final: 0.5743 (p-80) REVERT: C 97 GLU cc_start: 0.7138 (tp30) cc_final: 0.6860 (tp30) REVERT: C 152 ASN cc_start: 0.7488 (m110) cc_final: 0.6966 (p0) REVERT: C 279 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7993 (pttt) outliers start: 61 outliers final: 15 residues processed: 241 average time/residue: 0.6320 time to fit residues: 166.0721 Evaluate side-chains 156 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 HIS A 584 ASN B 55 GLN B 382 ASN B 409 GLN B 463 HIS B 584 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 331 ASN D 212 ASN D 303 HIS D 314 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107152 restraints weight = 21864.500| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.85 r_work: 0.3277 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13862 Z= 0.171 Angle : 0.565 6.746 18704 Z= 0.290 Chirality : 0.044 0.199 2087 Planarity : 0.004 0.038 2388 Dihedral : 6.847 142.086 1802 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.27 % Allowed : 16.40 % Favored : 79.33 % 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: -1.23 (0.20), residues: 1653 helix: 0.08 (0.20), residues: 631 sheet: -1.33 (0.26), residues: 382 loop : -1.22 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.016 0.002 TYR B 504 PHE 0.018 0.002 PHE A 104 TRP 0.013 0.002 TRP D 317 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13862) covalent geometry : angle 0.56481 / 0.29 (18704) hydrogen bonds : bond 0.03909 / 2.58 ( 582) hydrogen bonds : angle 5.04123 / 3.41 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 165 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 188 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8529 (ttpt) REVERT: A 262 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7171 (mm-30) REVERT: A 339 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8930 (tt) REVERT: A 352 ASP cc_start: 0.7581 (t0) cc_final: 0.7349 (t0) REVERT: A 532 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7107 (mp0) REVERT: A 559 GLU cc_start: 0.7701 (tt0) cc_final: 0.6806 (mt-10) REVERT: B 149 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: B 384 ILE cc_start: 0.8748 (mt) cc_final: 0.8470 (mm) REVERT: B 509 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8932 (tt) REVERT: C 78 HIS cc_start: 0.5953 (p-80) cc_final: 0.5733 (p-80) REVERT: C 207 GLN cc_start: 0.5262 (pm20) cc_final: 0.4428 (pm20) REVERT: C 288 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8276 (ttpp) REVERT: D 306 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7121 (pm20) outliers start: 64 outliers final: 24 residues processed: 203 average time/residue: 0.6297 time to fit residues: 139.5785 Evaluate side-chains 159 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 5.9990 chunk 159 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN A 382 ASN A 584 ASN B 14 GLN B 164 ASN B 276 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100060 restraints weight = 21980.856| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.82 r_work: 0.3163 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 13862 Z= 0.295 Angle : 0.671 7.587 18704 Z= 0.344 Chirality : 0.049 0.181 2087 Planarity : 0.004 0.049 2388 Dihedral : 7.321 140.623 1802 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.33 % Allowed : 16.80 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.20), residues: 1653 helix: 0.00 (0.20), residues: 641 sheet: -1.37 (0.26), residues: 382 loop : -1.33 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 32 TYR 0.017 0.002 TYR B 504 PHE 0.021 0.002 PHE D 261 TRP 0.013 0.002 TRP D 285 HIS 0.008 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.30 (13862) covalent geometry : angle 0.67144 / 0.34 (18704) hydrogen bonds : bond 0.04142 / 2.71 ( 582) hydrogen bonds : angle 5.16636 / 3.50 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 134 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 78 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8184 (tpt-90) REVERT: A 90 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8768 (mm) REVERT: A 166 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6142 (tpm-80) REVERT: A 188 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (ttpt) REVERT: A 262 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7107 (mm-30) REVERT: A 339 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 352 ASP cc_start: 0.7663 (t0) cc_final: 0.7416 (t0) REVERT: A 532 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7146 (mp0) REVERT: B 149 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: B 160 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8478 (tm) REVERT: B 349 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7825 (mm-30) REVERT: B 427 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 509 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8913 (tt) REVERT: B 656 GLU cc_start: 0.8024 (pp20) cc_final: 0.7739 (pp20) REVERT: C 68 ASP cc_start: 0.8567 (t0) cc_final: 0.8290 (t0) REVERT: C 78 HIS cc_start: 0.6027 (p-80) cc_final: 0.5806 (p-80) REVERT: C 97 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6768 (tp30) REVERT: C 137 GLN cc_start: 0.7936 (pp30) cc_final: 0.7706 (pp30) REVERT: C 144 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7958 (mmtt) REVERT: C 207 GLN cc_start: 0.5229 (pm20) cc_final: 0.4973 (pm20) REVERT: C 219 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: C 279 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8144 (tppt) REVERT: C 288 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8327 (ttpp) REVERT: C 309 HIS cc_start: 0.6975 (m-70) cc_final: 0.6742 (m170) REVERT: D 223 ASN cc_start: 0.8237 (m110) cc_final: 0.7472 (p0) REVERT: D 256 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: D 306 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7249 (pm20) outliers start: 80 outliers final: 32 residues processed: 201 average time/residue: 0.5988 time to fit residues: 131.5017 Evaluate side-chains 163 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 381 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 380 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 463 HIS B 631 GLN C 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104404 restraints weight = 21927.727| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.80 r_work: 0.3239 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13862 Z= 0.106 Angle : 0.515 6.759 18704 Z= 0.265 Chirality : 0.043 0.158 2087 Planarity : 0.003 0.040 2388 Dihedral : 6.884 132.877 1802 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.33 % Allowed : 19.20 % Favored : 77.47 % 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: -0.80 (0.21), residues: 1653 helix: 0.60 (0.21), residues: 630 sheet: -1.26 (0.26), residues: 382 loop : -1.06 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.014 0.001 TYR B 504 PHE 0.016 0.001 PHE A 104 TRP 0.012 0.001 TRP D 242 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (13862) covalent geometry : angle 0.51475 / 0.27 (18704) hydrogen bonds : bond 0.03157 / 2.08 ( 582) hydrogen bonds : angle 4.80267 / 3.24 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8710 (t) REVERT: A 29 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 165 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: A 188 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8646 (ttpt) REVERT: A 314 ARG cc_start: 0.8775 (mpp80) cc_final: 0.8399 (mpp-170) REVERT: A 339 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8886 (tt) REVERT: A 352 ASP cc_start: 0.7652 (t0) cc_final: 0.7403 (t0) REVERT: A 532 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7097 (mp0) REVERT: B 349 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7698 (mm-30) REVERT: B 427 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 509 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8988 (tt) REVERT: B 548 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7880 (mtmm) REVERT: B 559 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: C 68 ASP cc_start: 0.8326 (t0) cc_final: 0.7802 (t0) REVERT: C 97 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: C 137 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7790 (pp30) REVERT: C 279 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8142 (tppt) REVERT: C 288 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8537 (tttt) REVERT: D 306 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7224 (pm20) outliers start: 50 outliers final: 14 residues processed: 191 average time/residue: 0.6401 time to fit residues: 133.0592 Evaluate side-chains 150 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 382 ASN B 463 HIS B 631 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100810 restraints weight = 21933.277| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.78 r_work: 0.3180 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13862 Z= 0.222 Angle : 0.596 8.260 18704 Z= 0.308 Chirality : 0.046 0.213 2087 Planarity : 0.004 0.041 2388 Dihedral : 7.122 138.951 1802 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.60 % Allowed : 19.47 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.20), residues: 1653 helix: 0.51 (0.21), residues: 634 sheet: -1.30 (0.26), residues: 382 loop : -1.03 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 666 TYR 0.016 0.002 TYR B 203 PHE 0.017 0.002 PHE D 261 TRP 0.011 0.002 TRP D 285 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (13862) covalent geometry : angle 0.59611 / 0.31 (18704) hydrogen bonds : bond 0.03671 / 2.42 ( 582) hydrogen bonds : angle 4.89735 / 3.30 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 165 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: A 188 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8718 (ttpt) REVERT: A 314 ARG cc_start: 0.8811 (mpp80) cc_final: 0.8463 (mpp-170) REVERT: A 339 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 352 ASP cc_start: 0.7700 (t0) cc_final: 0.7415 (t0) REVERT: A 532 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7019 (mp0) REVERT: A 637 ASP cc_start: 0.7803 (t0) cc_final: 0.7554 (m-30) REVERT: B 349 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7762 (mm-30) REVERT: B 367 SER cc_start: 0.7880 (t) cc_final: 0.7568 (p) REVERT: B 427 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 509 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 548 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8044 (mtmm) REVERT: C 68 ASP cc_start: 0.8446 (t0) cc_final: 0.7998 (t0) REVERT: C 97 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6669 (tp30) REVERT: C 279 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8178 (tppt) REVERT: C 288 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8280 (ttpp) REVERT: D 256 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: D 306 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7285 (pm20) outliers start: 54 outliers final: 23 residues processed: 175 average time/residue: 0.5466 time to fit residues: 105.6682 Evaluate side-chains 148 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 53 optimal weight: 0.0470 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 463 HIS B 631 GLN C 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102736 restraints weight = 21765.852| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.77 r_work: 0.3215 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13862 Z= 0.132 Angle : 0.537 9.039 18704 Z= 0.277 Chirality : 0.043 0.169 2087 Planarity : 0.004 0.041 2388 Dihedral : 6.972 134.800 1802 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.87 % Allowed : 19.87 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1653 helix: 0.67 (0.21), residues: 633 sheet: -1.29 (0.26), residues: 372 loop : -0.89 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 666 TYR 0.014 0.001 TYR B 504 PHE 0.013 0.001 PHE A 104 TRP 0.011 0.001 TRP D 242 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (13862) covalent geometry : angle 0.53672 / 0.28 (18704) hydrogen bonds : bond 0.03208 / 2.11 ( 582) hydrogen bonds : angle 4.78283 / 3.21 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 188 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8689 (ttpt) REVERT: A 314 ARG cc_start: 0.8785 (mpp80) cc_final: 0.8447 (mpp-170) REVERT: A 339 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8905 (tt) REVERT: A 352 ASP cc_start: 0.7629 (t0) cc_final: 0.7327 (t0) REVERT: A 532 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7042 (mp0) REVERT: A 635 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.7067 (p) REVERT: A 637 ASP cc_start: 0.7747 (t0) cc_final: 0.7525 (m-30) REVERT: B 195 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8575 (tmmm) REVERT: B 349 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7717 (mm-30) REVERT: B 427 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 503 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7393 (tp30) REVERT: B 509 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9010 (tt) REVERT: B 548 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7933 (mtmm) REVERT: B 568 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7955 (mp) REVERT: C 68 ASP cc_start: 0.8376 (t0) cc_final: 0.7841 (t0) REVERT: C 97 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6589 (tp30) REVERT: C 207 GLN cc_start: 0.5163 (pm20) cc_final: 0.4514 (pt0) REVERT: C 279 LYS cc_start: 0.8430 (mmmt) cc_final: 0.8165 (tppt) REVERT: C 288 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8260 (ttpp) REVERT: D 256 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: D 306 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7282 (pm20) outliers start: 43 outliers final: 20 residues processed: 162 average time/residue: 0.5664 time to fit residues: 101.0679 Evaluate side-chains 145 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 382 ASN B 463 HIS B 631 GLN C 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103574 restraints weight = 21715.701| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.77 r_work: 0.3226 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13862 Z= 0.117 Angle : 0.523 8.278 18704 Z= 0.271 Chirality : 0.043 0.166 2087 Planarity : 0.004 0.050 2388 Dihedral : 6.904 133.259 1802 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 19.87 % Favored : 77.27 % 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: -0.61 (0.21), residues: 1653 helix: 0.72 (0.21), residues: 633 sheet: -1.28 (0.27), residues: 370 loop : -0.84 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 666 TYR 0.015 0.001 TYR B 504 PHE 0.013 0.001 PHE A 104 TRP 0.012 0.001 TRP D 242 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13862) covalent geometry : angle 0.52330 / 0.27 (18704) hydrogen bonds : bond 0.03088 / 2.04 ( 582) hydrogen bonds : angle 4.70701 / 3.16 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 188 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8684 (ttpt) REVERT: A 314 ARG cc_start: 0.8751 (mpp80) cc_final: 0.8383 (mpp-170) REVERT: A 339 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8904 (tt) REVERT: A 352 ASP cc_start: 0.7633 (t0) cc_final: 0.7329 (t0) REVERT: A 532 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7050 (mp0) REVERT: A 635 VAL cc_start: 0.7345 (OUTLIER) cc_final: 0.7039 (p) REVERT: A 637 ASP cc_start: 0.7712 (t0) cc_final: 0.7483 (m-30) REVERT: B 195 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8578 (tmmm) REVERT: B 349 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7658 (mm-30) REVERT: B 367 SER cc_start: 0.7773 (t) cc_final: 0.7510 (p) REVERT: B 427 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 503 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7377 (tp30) REVERT: B 509 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9026 (tt) REVERT: B 548 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7939 (mtmm) REVERT: B 559 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: B 568 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 68 ASP cc_start: 0.8330 (t0) cc_final: 0.7888 (t0) REVERT: C 70 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7738 (pptt) REVERT: C 207 GLN cc_start: 0.5074 (pm20) cc_final: 0.4471 (pt0) REVERT: C 279 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8125 (tppt) REVERT: C 288 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8546 (tttt) REVERT: D 306 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7239 (pm20) outliers start: 43 outliers final: 21 residues processed: 164 average time/residue: 0.5628 time to fit residues: 102.0139 Evaluate side-chains 147 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 142 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS B 578 GLN B 631 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102763 restraints weight = 21829.771| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.77 r_work: 0.3216 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13862 Z= 0.142 Angle : 0.551 9.563 18704 Z= 0.283 Chirality : 0.043 0.166 2087 Planarity : 0.004 0.047 2388 Dihedral : 6.944 134.776 1802 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.53 % Allowed : 20.73 % Favored : 76.73 % 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: -0.58 (0.21), residues: 1653 helix: 0.70 (0.21), residues: 633 sheet: -1.21 (0.27), residues: 358 loop : -0.82 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 666 TYR 0.016 0.001 TYR B 504 PHE 0.013 0.001 PHE D 261 TRP 0.013 0.001 TRP C 9 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13862) covalent geometry : angle 0.55092 / 0.28 (18704) hydrogen bonds : bond 0.03198 / 2.11 ( 582) hydrogen bonds : angle 4.71711 / 3.17 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 188 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8702 (ttpt) REVERT: A 314 ARG cc_start: 0.8786 (mpp80) cc_final: 0.8438 (mpp-170) REVERT: A 339 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 352 ASP cc_start: 0.7645 (t0) cc_final: 0.7412 (t0) REVERT: A 532 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7061 (mp0) REVERT: A 544 GLU cc_start: 0.8187 (tp30) cc_final: 0.7598 (tp30) REVERT: A 635 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7068 (p) REVERT: A 637 ASP cc_start: 0.7680 (t0) cc_final: 0.7448 (m-30) REVERT: B 195 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8604 (tmmm) REVERT: B 349 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7635 (mm-30) REVERT: B 367 SER cc_start: 0.7797 (t) cc_final: 0.7550 (p) REVERT: B 427 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 503 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7356 (tp30) REVERT: B 509 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8994 (tt) REVERT: B 559 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: B 568 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (mp) REVERT: C 68 ASP cc_start: 0.8426 (t0) cc_final: 0.8015 (t0) REVERT: C 70 LYS cc_start: 0.8201 (ptmm) cc_final: 0.7764 (pptt) REVERT: C 207 GLN cc_start: 0.5009 (pm20) cc_final: 0.4427 (pt0) REVERT: C 279 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8134 (tppt) REVERT: C 288 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8531 (tttt) REVERT: D 256 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: D 306 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7261 (pm20) outliers start: 38 outliers final: 22 residues processed: 159 average time/residue: 0.5489 time to fit residues: 96.5584 Evaluate side-chains 145 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 4.9990 chunk 103 optimal weight: 0.0270 chunk 155 optimal weight: 0.0270 chunk 7 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 463 HIS B 631 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101880 restraints weight = 21928.203| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.77 r_work: 0.3199 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13862 Z= 0.170 Angle : 0.569 8.671 18704 Z= 0.293 Chirality : 0.044 0.167 2087 Planarity : 0.004 0.052 2388 Dihedral : 7.037 136.873 1802 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.60 % Allowed : 20.87 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1653 helix: 0.64 (0.21), residues: 634 sheet: -1.21 (0.27), residues: 358 loop : -0.83 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 666 TYR 0.017 0.002 TYR B 504 PHE 0.033 0.001 PHE B 579 TRP 0.011 0.001 TRP C 9 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (13862) covalent geometry : angle 0.56923 / 0.29 (18704) hydrogen bonds : bond 0.03361 / 2.20 ( 582) hydrogen bonds : angle 4.78870 / 3.22 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 188 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (ttpt) REVERT: A 314 ARG cc_start: 0.8816 (mpp80) cc_final: 0.8499 (mpp-170) REVERT: A 339 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8923 (tt) REVERT: A 352 ASP cc_start: 0.7637 (t0) cc_final: 0.7414 (t0) REVERT: A 532 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7086 (mp0) REVERT: A 544 GLU cc_start: 0.8226 (tp30) cc_final: 0.7651 (tp30) REVERT: A 635 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7071 (p) REVERT: A 637 ASP cc_start: 0.7706 (t0) cc_final: 0.7472 (m-30) REVERT: B 14 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7532 (mm110) REVERT: B 195 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8595 (tmmm) REVERT: B 349 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7646 (mm-30) REVERT: B 367 SER cc_start: 0.7827 (t) cc_final: 0.7577 (p) REVERT: B 427 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: B 509 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8980 (tt) REVERT: B 548 LYS cc_start: 0.8397 (ttmm) cc_final: 0.7985 (mtmm) REVERT: B 559 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: B 568 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7986 (mp) REVERT: C 68 ASP cc_start: 0.8451 (t0) cc_final: 0.8064 (t0) REVERT: C 70 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7773 (pptt) REVERT: C 279 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8141 (tppt) REVERT: C 288 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8548 (tttt) REVERT: D 256 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: D 306 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7263 (pm20) outliers start: 39 outliers final: 24 residues processed: 148 average time/residue: 0.5010 time to fit residues: 82.4984 Evaluate side-chains 140 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 157 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 0.0370 chunk 52 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 463 HIS B 631 GLN C 303 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102097 restraints weight = 21930.545| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.78 r_work: 0.3201 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13862 Z= 0.158 Angle : 0.564 8.609 18704 Z= 0.290 Chirality : 0.044 0.167 2087 Planarity : 0.004 0.048 2388 Dihedral : 7.025 136.401 1802 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.80 % Allowed : 20.73 % Favored : 76.47 % 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: -0.61 (0.21), residues: 1653 helix: 0.66 (0.21), residues: 634 sheet: -1.22 (0.27), residues: 358 loop : -0.82 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 666 TYR 0.017 0.001 TYR A 203 PHE 0.035 0.001 PHE B 579 TRP 0.011 0.001 TRP C 9 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13862) covalent geometry : angle 0.56418 / 0.29 (18704) hydrogen bonds : bond 0.03313 / 2.17 ( 582) hydrogen bonds : angle 4.78407 / 3.22 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4759.48 seconds wall clock time: 82 minutes 1.00 seconds (4921.00 seconds total)