Starting phenix.real_space_refine on Thu Sep 18 03:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlh_22244/09_2025/6xlh_22244.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlh_22244/09_2025/6xlh_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_2025/6xlh_22244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2025/6xlh_22244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2025/6xlh_22244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlh_22244/09_2025/6xlh_22244.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.63, per 1000 atoms: 0.27 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: 1.26 Conformation dependent library (CDL) restraints added in 716.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 2.62 Time building geometry restraints manager: 1.62 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: 8413 33.51 - 67.01: 30 67.01 - 100.52: 0 100.52 - 134.03: 2 134.03 - 167.53: 1 Dihedral angle restraints: 8446 sinusoidal: 3542 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 8443 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.800 Find NCS groups from input model: 0.150 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 7.607 167.535 5254 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 aren 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 covalent geometry : bond 0.00118 (13862) covalent geometry : angle 0.38769 (18704) hydrogen bonds : bond 0.26959 ( 582) hydrogen bonds : angle 8.36180 ( 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 : 0.548 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: 0.7931 time to fit residues: 403.9986 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 : 0.585 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.132535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113408 restraints weight = 21750.966| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.76 r_work: 0.3376 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13862 Z= 0.177 Angle : 0.600 6.668 18704 Z= 0.312 Chirality : 0.045 0.168 2087 Planarity : 0.004 0.044 2388 Dihedral : 6.884 157.175 1813 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.20 % Allowed : 14.93 % 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 aren not related in a simple way. whole: -1.89 (0.19), residues: 1653 helix: -0.76 (0.19), residues: 624 sheet: -1.35 (0.25), residues: 386 loop : -1.48 (0.23), 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 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00407 (13862) covalent geometry : angle 0.59978 (18704) hydrogen bonds : bond 0.04409 ( 582) hydrogen bonds : angle 5.45807 ( 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 258 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 165 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: A 262 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7014 (mm-30) REVERT: A 339 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 384 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7951 (pt) REVERT: A 480 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8211 (mppt) REVERT: A 559 GLU cc_start: 0.7616 (tt0) cc_final: 0.6840 (mt-10) REVERT: B 543 TYR cc_start: 0.7877 (m-80) cc_final: 0.7638 (m-80) REVERT: B 548 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7974 (ttmm) REVERT: B 559 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: C 78 HIS cc_start: 0.5986 (p-80) cc_final: 0.5743 (p-80) REVERT: C 97 GLU cc_start: 0.7135 (tp30) cc_final: 0.6842 (tp30) REVERT: C 144 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7841 (mmtt) REVERT: C 152 ASN cc_start: 0.7494 (m110) cc_final: 0.6972 (p0) REVERT: C 279 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7997 (pttt) outliers start: 63 outliers final: 15 residues processed: 242 average time/residue: 0.6832 time to fit residues: 179.7065 Evaluate side-chains 160 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 144 LYS 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: 0.0020 chunk 116 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 GLN A 463 HIS A 584 ASN B 55 GLN B 382 ASN B 463 HIS B 584 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN D 212 ASN D 303 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111741 restraints weight = 21948.755| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.82 r_work: 0.3346 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13862 Z= 0.116 Angle : 0.517 8.087 18704 Z= 0.265 Chirality : 0.043 0.151 2087 Planarity : 0.003 0.039 2388 Dihedral : 6.804 146.432 1813 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.60 % Allowed : 16.53 % Favored : 79.87 % 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 aren not related in a simple way. whole: -1.12 (0.20), residues: 1653 helix: 0.16 (0.21), residues: 625 sheet: -1.29 (0.25), residues: 386 loop : -1.13 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.016 0.001 TYR B 504 PHE 0.017 0.001 PHE A 104 TRP 0.009 0.001 TRP A 581 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00262 (13862) covalent geometry : angle 0.51698 (18704) hydrogen bonds : bond 0.03669 ( 582) hydrogen bonds : angle 5.00871 ( 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 219 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 77 ILE cc_start: 0.9335 (mt) cc_final: 0.9131 (mt) REVERT: A 165 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: A 188 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8482 (ttpt) REVERT: A 262 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7169 (mm-30) REVERT: A 339 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 352 ASP cc_start: 0.7531 (t0) cc_final: 0.7317 (t0) REVERT: A 384 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7896 (pt) REVERT: A 532 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7132 (mp0) REVERT: A 559 GLU cc_start: 0.7670 (tt0) cc_final: 0.6874 (mt-10) REVERT: A 626 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6627 (p0) REVERT: B 149 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: B 509 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 559 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: C 78 HIS cc_start: 0.6000 (p-80) cc_final: 0.5781 (p-80) REVERT: C 207 GLN cc_start: 0.5241 (pm20) cc_final: 0.4656 (pt0) REVERT: C 288 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8241 (ttpp) REVERT: D 306 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7042 (pm20) outliers start: 54 outliers final: 18 residues processed: 203 average time/residue: 0.6347 time to fit residues: 141.1001 Evaluate side-chains 161 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 A residue 626 ASP 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 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 559 GLU Chi-restraints excluded: chain C residue 46 SER 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 324 GLU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** 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** B 14 GLN B 164 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 463 HIS C 78 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN 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 = 0.120258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099850 restraints weight = 22007.633| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.81 r_work: 0.3161 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 13862 Z= 0.319 Angle : 0.711 8.102 18704 Z= 0.363 Chirality : 0.050 0.191 2087 Planarity : 0.005 0.040 2388 Dihedral : 7.555 141.334 1813 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.20 % Allowed : 16.33 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.20), residues: 1653 helix: -0.00 (0.20), residues: 629 sheet: -1.34 (0.26), residues: 382 loop : -1.25 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 389 TYR 0.019 0.002 TYR B 504 PHE 0.025 0.002 PHE D 261 TRP 0.016 0.002 TRP D 285 HIS 0.009 0.002 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00760 (13862) covalent geometry : angle 0.71061 (18704) hydrogen bonds : bond 0.04380 ( 582) hydrogen bonds : angle 5.24548 ( 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 218 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 140 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 90 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8776 (mm) REVERT: A 166 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6156 (tpm-80) REVERT: A 188 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (ttpt) REVERT: A 262 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7100 (mm-30) REVERT: A 339 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8956 (tt) REVERT: A 352 ASP cc_start: 0.7623 (t0) cc_final: 0.7377 (t0) REVERT: A 532 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7164 (mp0) REVERT: B 149 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: B 160 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8472 (tm) REVERT: B 162 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: B 349 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7847 (mm-30) REVERT: B 382 ASN cc_start: 0.6500 (m-40) cc_final: 0.6298 (t0) REVERT: B 383 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7688 (mmtt) REVERT: B 427 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: B 548 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8059 (tppt) REVERT: B 656 GLU cc_start: 0.7876 (pp20) cc_final: 0.7642 (pp20) REVERT: C 97 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6743 (tp30) REVERT: C 207 GLN cc_start: 0.5214 (pm20) cc_final: 0.4891 (pm20) REVERT: C 219 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: C 238 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7991 (ttt90) REVERT: C 309 HIS cc_start: 0.6969 (m-70) cc_final: 0.6730 (m170) REVERT: C 324 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: D 223 ASN cc_start: 0.8226 (m110) cc_final: 0.7484 (p0) REVERT: D 306 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7256 (pm20) outliers start: 78 outliers final: 31 residues processed: 207 average time/residue: 0.7046 time to fit residues: 158.5650 Evaluate side-chains 156 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 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 162 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 383 LYS 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 533 LYS Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 46 SER 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 164 ASN Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 238 ARG 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 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: 3.9990 chunk 158 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN B 14 GLN B 276 ASN B 380 GLN B 463 HIS B 631 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103987 restraints weight = 21850.500| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.81 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13862 Z= 0.116 Angle : 0.527 7.938 18704 Z= 0.271 Chirality : 0.043 0.160 2087 Planarity : 0.003 0.037 2388 Dihedral : 7.063 134.911 1813 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.13 % Allowed : 19.40 % 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 aren not related in a simple way. whole: -0.85 (0.20), residues: 1653 helix: 0.53 (0.21), residues: 628 sheet: -1.27 (0.26), residues: 384 loop : -1.05 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.016 0.001 TYR B 504 PHE 0.015 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 covalent geometry : bond 0.00263 (13862) covalent geometry : angle 0.52749 (18704) hydrogen bonds : bond 0.03259 ( 582) hydrogen bonds : angle 4.85948 ( 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 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8695 (t) REVERT: A 29 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 78 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8172 (tpt-90) REVERT: A 165 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: A 188 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8641 (ttpt) REVERT: A 339 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8889 (tt) REVERT: A 352 ASP cc_start: 0.7617 (t0) cc_final: 0.7370 (t0) REVERT: A 532 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7088 (mp0) REVERT: B 349 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7706 (mm-30) REVERT: C 68 ASP cc_start: 0.8344 (t0) cc_final: 0.7930 (t0) REVERT: C 97 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6902 (tp30) REVERT: C 219 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: C 288 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8226 (ttpp) REVERT: D 306 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7230 (pm20) outliers start: 47 outliers final: 16 residues processed: 182 average time/residue: 0.7230 time to fit residues: 142.7289 Evaluate side-chains 145 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 78 ARG 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 471 THR Chi-restraints excluded: chain A residue 594 LEU 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 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 141 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN B 14 GLN B 382 ASN B 463 HIS B 631 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104714 restraints weight = 21850.590| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.81 r_work: 0.3243 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13862 Z= 0.110 Angle : 0.526 8.299 18704 Z= 0.271 Chirality : 0.043 0.204 2087 Planarity : 0.004 0.039 2388 Dihedral : 6.967 135.559 1813 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.93 % Allowed : 20.13 % 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 aren not related in a simple way. whole: -0.63 (0.21), residues: 1653 helix: 0.71 (0.21), residues: 632 sheet: -1.17 (0.26), residues: 381 loop : -0.93 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 666 TYR 0.014 0.001 TYR B 203 PHE 0.016 0.001 PHE A 104 TRP 0.012 0.001 TRP C 9 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00252 (13862) covalent geometry : angle 0.52594 (18704) hydrogen bonds : bond 0.03086 ( 582) hydrogen bonds : angle 4.69283 ( 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 179 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8461 (mp) REVERT: A 165 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 188 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8640 (ttpt) REVERT: A 339 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8892 (tt) REVERT: A 352 ASP cc_start: 0.7584 (t0) cc_final: 0.7302 (t0) REVERT: A 430 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: A 532 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7087 (mp0) REVERT: B 349 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7658 (mm-30) REVERT: B 367 SER cc_start: 0.7722 (t) cc_final: 0.7427 (p) REVERT: B 384 ILE cc_start: 0.8790 (mt) cc_final: 0.8510 (mm) REVERT: B 559 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: C 207 GLN cc_start: 0.5227 (pm20) cc_final: 0.4696 (pt0) REVERT: C 288 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8193 (ttpp) REVERT: D 306 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7227 (pm20) outliers start: 44 outliers final: 16 residues processed: 169 average time/residue: 0.6090 time to fit residues: 113.0427 Evaluate side-chains 143 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 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 165 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 297 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 471 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 594 LEU 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 382 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS 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: 6.9990 chunk 19 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 380 GLN A 381 GLN B 14 GLN B 463 HIS B 631 GLN C 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105418 restraints weight = 21751.433| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.76 r_work: 0.3263 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13862 Z= 0.099 Angle : 0.504 8.033 18704 Z= 0.259 Chirality : 0.042 0.172 2087 Planarity : 0.004 0.039 2388 Dihedral : 6.885 136.359 1813 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.60 % Allowed : 20.27 % Favored : 77.13 % 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 aren not related in a simple way. whole: -0.51 (0.21), residues: 1653 helix: 0.80 (0.21), residues: 633 sheet: -1.14 (0.26), residues: 381 loop : -0.84 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 666 TYR 0.013 0.001 TYR B 504 PHE 0.014 0.001 PHE A 104 TRP 0.011 0.001 TRP C 9 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00219 (13862) covalent geometry : angle 0.50449 (18704) hydrogen bonds : bond 0.02939 ( 582) hydrogen bonds : angle 4.62020 ( 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 176 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 188 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8631 (ttpt) REVERT: A 339 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 352 ASP cc_start: 0.7561 (t0) cc_final: 0.7311 (t0) REVERT: A 430 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: A 532 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7024 (mp0) REVERT: B 367 SER cc_start: 0.7847 (t) cc_final: 0.7521 (p) REVERT: B 382 ASN cc_start: 0.5693 (OUTLIER) cc_final: 0.5485 (t0) REVERT: B 383 LYS cc_start: 0.7658 (mmmt) cc_final: 0.7432 (mmtt) REVERT: B 503 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7461 (tp30) REVERT: B 559 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: C 68 ASP cc_start: 0.8216 (t0) cc_final: 0.7806 (t0) REVERT: C 108 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6593 (mm-40) REVERT: C 207 GLN cc_start: 0.5101 (pm20) cc_final: 0.4678 (pt0) REVERT: C 288 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8310 (ttpp) REVERT: D 306 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7216 (pm20) outliers start: 39 outliers final: 11 residues processed: 169 average time/residue: 0.5871 time to fit residues: 109.3146 Evaluate side-chains 144 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 471 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 0.0980 chunk 156 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 GLN B 382 ASN B 463 HIS B 631 GLN C 137 GLN D 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106244 restraints weight = 21756.251| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.77 r_work: 0.3269 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13862 Z= 0.100 Angle : 0.511 9.938 18704 Z= 0.262 Chirality : 0.042 0.167 2087 Planarity : 0.004 0.039 2388 Dihedral : 6.840 136.453 1813 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.40 % Allowed : 20.80 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.21), residues: 1653 helix: 0.85 (0.21), residues: 633 sheet: -1.16 (0.27), residues: 369 loop : -0.76 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 666 TYR 0.014 0.001 TYR B 203 PHE 0.012 0.001 PHE A 104 TRP 0.011 0.001 TRP C 9 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00228 (13862) covalent geometry : angle 0.51061 (18704) hydrogen bonds : bond 0.02869 ( 582) hydrogen bonds : angle 4.56066 ( 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 178 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 188 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8637 (ttpt) REVERT: A 314 ARG cc_start: 0.8823 (mpp80) cc_final: 0.8430 (mpp-170) REVERT: A 339 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 352 ASP cc_start: 0.7553 (t0) cc_final: 0.7296 (t0) REVERT: A 430 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: A 532 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7021 (mp0) REVERT: A 635 VAL cc_start: 0.7309 (t) cc_final: 0.7087 (p) REVERT: B 503 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7461 (tp30) REVERT: B 559 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: C 68 ASP cc_start: 0.8233 (t0) cc_final: 0.7837 (t0) REVERT: C 70 LYS cc_start: 0.8099 (ptmm) cc_final: 0.7665 (pptt) REVERT: C 108 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6557 (mm-40) REVERT: C 207 GLN cc_start: 0.4970 (pm20) cc_final: 0.4645 (pt0) REVERT: D 306 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7156 (pm20) outliers start: 36 outliers final: 17 residues processed: 169 average time/residue: 0.5563 time to fit residues: 103.8169 Evaluate side-chains 149 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 56 LEU 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 471 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 626 ASP 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 180 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 218 LEU 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: 3.9990 chunk 20 optimal weight: 0.0870 chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS B 631 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106123 restraints weight = 21837.680| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.77 r_work: 0.3265 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13862 Z= 0.108 Angle : 0.515 9.055 18704 Z= 0.265 Chirality : 0.043 0.166 2087 Planarity : 0.004 0.039 2388 Dihedral : 6.854 136.089 1813 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 21.27 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.21), residues: 1653 helix: 0.88 (0.21), residues: 633 sheet: -1.10 (0.27), residues: 369 loop : -0.74 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 666 TYR 0.020 0.001 TYR C 23 PHE 0.014 0.001 PHE A 104 TRP 0.011 0.001 TRP C 9 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00249 (13862) covalent geometry : angle 0.51471 (18704) hydrogen bonds : bond 0.02916 ( 582) hydrogen bonds : angle 4.56199 ( 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 162 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 188 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8636 (ttpt) REVERT: A 314 ARG cc_start: 0.8816 (mpp80) cc_final: 0.8431 (mpp-170) REVERT: A 339 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8903 (tt) REVERT: A 352 ASP cc_start: 0.7632 (t0) cc_final: 0.7342 (t0) REVERT: A 430 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: A 532 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7085 (mp0) REVERT: A 635 VAL cc_start: 0.7353 (t) cc_final: 0.7098 (p) REVERT: B 367 SER cc_start: 0.7882 (t) cc_final: 0.7660 (p) REVERT: B 384 ILE cc_start: 0.8759 (mt) cc_final: 0.8498 (mm) REVERT: B 503 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7441 (tp30) REVERT: B 559 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: C 68 ASP cc_start: 0.8277 (t0) cc_final: 0.7859 (t0) REVERT: C 70 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7687 (pptt) REVERT: C 108 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6520 (mm-40) REVERT: C 207 GLN cc_start: 0.4919 (pm20) cc_final: 0.4598 (pt0) REVERT: D 306 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7152 (pm20) outliers start: 29 outliers final: 18 residues processed: 155 average time/residue: 0.5646 time to fit residues: 96.3504 Evaluate side-chains 146 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 56 LEU 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 339 LEU 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 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 180 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 218 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS B 631 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104934 restraints weight = 21844.009| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.75 r_work: 0.3250 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13862 Z= 0.129 Angle : 0.534 8.611 18704 Z= 0.274 Chirality : 0.043 0.165 2087 Planarity : 0.004 0.040 2388 Dihedral : 6.945 134.758 1813 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.73 % Allowed : 21.47 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.21), residues: 1653 helix: 0.82 (0.21), residues: 634 sheet: -1.09 (0.27), residues: 369 loop : -0.72 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 666 TYR 0.018 0.001 TYR C 23 PHE 0.013 0.001 PHE A 104 TRP 0.012 0.001 TRP C 9 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00300 (13862) covalent geometry : angle 0.53416 (18704) hydrogen bonds : bond 0.03079 ( 582) hydrogen bonds : angle 4.61366 ( 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 154 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 188 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8645 (ttpt) REVERT: A 314 ARG cc_start: 0.8819 (mpp80) cc_final: 0.8433 (mpp-170) REVERT: A 339 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8909 (tt) REVERT: A 352 ASP cc_start: 0.7645 (t0) cc_final: 0.7336 (t0) REVERT: A 430 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: A 532 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7056 (mp0) REVERT: B 367 SER cc_start: 0.7938 (t) cc_final: 0.7726 (p) REVERT: B 384 ILE cc_start: 0.8763 (mt) cc_final: 0.8514 (mm) REVERT: B 503 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7387 (tp30) REVERT: B 548 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8067 (mtmm) REVERT: C 68 ASP cc_start: 0.8313 (t0) cc_final: 0.7939 (t0) REVERT: C 70 LYS cc_start: 0.8168 (ptmm) cc_final: 0.7715 (pptt) REVERT: C 108 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6563 (mm-40) REVERT: C 207 GLN cc_start: 0.4972 (pm20) cc_final: 0.4632 (pt0) REVERT: D 306 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7171 (pm20) outliers start: 26 outliers final: 17 residues processed: 148 average time/residue: 0.5324 time to fit residues: 87.7054 Evaluate side-chains 141 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 56 LEU 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 339 LEU 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 B residue 74 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 218 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 157 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 ASN 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 = 0.3648 r_free = 0.3648 target = 0.124427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104421 restraints weight = 21890.023| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.77 r_work: 0.3239 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13862 Z= 0.133 Angle : 0.546 10.596 18704 Z= 0.278 Chirality : 0.044 0.162 2087 Planarity : 0.004 0.040 2388 Dihedral : 6.976 134.281 1813 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 21.47 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1653 helix: 0.83 (0.21), residues: 633 sheet: -1.09 (0.27), residues: 370 loop : -0.70 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 666 TYR 0.018 0.001 TYR C 23 PHE 0.013 0.001 PHE D 261 TRP 0.014 0.001 TRP C 9 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00311 (13862) covalent geometry : angle 0.54565 (18704) hydrogen bonds : bond 0.03084 ( 582) hydrogen bonds : angle 4.63807 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5199.45 seconds wall clock time: 89 minutes 29.33 seconds (5369.33 seconds total)