Starting phenix.real_space_refine on Thu Sep 26 18:38:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/09_2024/6xlh_22244.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/09_2024/6xlh_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/09_2024/6xlh_22244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/09_2024/6xlh_22244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/09_2024/6xlh_22244.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/09_2024/6xlh_22244.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.99, per 1000 atoms: 0.66 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.70 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: 4.77 Time building geometry restraints manager: 3.90 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.570 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- 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= 0.077 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 273 HIS 0.001 0.000 HIS B 304 PHE 0.004 0.000 PHE A 609 TYR 0.008 0.000 TYR A 24 ARG 0.001 0.000 ARG A 322 *********************** 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 fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 1.565 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: 1.4891 time to fit residues: 761.4181 Evaluate side-chains 193 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 463 HIS B 14 GLN B 26 ASN B 55 GLN B 91 ASN B 335 ASN B 463 HIS C 4 ASN C 57 ASN C 94 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 267 ASN C 306 GLN D 207 GLN D 303 HIS D 314 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13862 Z= 0.389 Angle : 0.671 7.262 18704 Z= 0.353 Chirality : 0.048 0.198 2087 Planarity : 0.005 0.043 2388 Dihedral : 7.061 152.475 1813 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.53 % Allowed : 14.47 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1653 helix: -0.82 (0.18), residues: 624 sheet: -1.39 (0.25), residues: 382 loop : -1.50 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 285 HIS 0.008 0.002 HIS A 463 PHE 0.018 0.002 PHE C 264 TYR 0.013 0.002 TYR C 23 ARG 0.010 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 189 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 165 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: A 211 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7771 (mmtm) REVERT: A 339 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 368 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5784 (tm-30) REVERT: A 559 GLU cc_start: 0.6574 (tt0) cc_final: 0.6333 (mt-10) REVERT: A 623 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7423 (mptt) REVERT: B 149 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 377 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: B 427 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: B 559 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: C 207 GLN cc_start: 0.4872 (pm20) cc_final: 0.4408 (pm20) REVERT: C 288 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8158 (ttpp) REVERT: C 301 THR cc_start: 0.8518 (m) cc_final: 0.8301 (m) outliers start: 68 outliers final: 21 residues processed: 241 average time/residue: 1.3769 time to fit residues: 360.2687 Evaluate side-chains 164 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 211 LYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 GLU 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 B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 377 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 559 GLU Chi-restraints excluded: chain C residue 46 SER 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 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 280 LYS 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 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 335 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 409 GLN B 463 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13862 Z= 0.291 Angle : 0.587 7.410 18704 Z= 0.301 Chirality : 0.045 0.156 2087 Planarity : 0.004 0.039 2388 Dihedral : 7.106 138.544 1813 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.80 % Allowed : 16.07 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1653 helix: -0.01 (0.20), residues: 629 sheet: -1.43 (0.26), residues: 376 loop : -1.24 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 285 HIS 0.006 0.001 HIS C 78 PHE 0.018 0.002 PHE A 104 TYR 0.019 0.002 TYR B 504 ARG 0.004 0.001 ARG A 174 *********************** 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 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 148 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 78 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7850 (tpt-90) REVERT: A 165 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: A 166 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6168 (tpm-80) REVERT: A 188 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: A 339 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 149 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: B 384 ILE cc_start: 0.8591 (mt) cc_final: 0.8345 (mm) REVERT: C 68 ASP cc_start: 0.7727 (t0) cc_final: 0.7434 (t0) REVERT: C 97 GLU cc_start: 0.6939 (tp30) cc_final: 0.6576 (tp30) REVERT: C 288 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: D 256 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7176 (mm-30) outliers start: 72 outliers final: 28 residues processed: 208 average time/residue: 1.2803 time to fit residues: 291.5205 Evaluate side-chains 153 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 166 ARG 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 484 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 667 LEU 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 113 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 276 ASN B 335 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13862 Z= 0.212 Angle : 0.542 6.980 18704 Z= 0.280 Chirality : 0.044 0.165 2087 Planarity : 0.004 0.040 2388 Dihedral : 7.023 134.918 1813 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.13 % Allowed : 17.93 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1653 helix: 0.39 (0.21), residues: 628 sheet: -1.41 (0.25), residues: 382 loop : -1.17 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 285 HIS 0.003 0.001 HIS A 463 PHE 0.017 0.001 PHE A 104 TYR 0.017 0.001 TYR B 504 ARG 0.003 0.000 ARG A 314 *********************** 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 195 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 133 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8242 (mp) REVERT: A 165 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: A 166 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6139 (tpm-80) REVERT: A 188 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8146 (ttpt) REVERT: A 339 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 335 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6599 (m-40) REVERT: B 427 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: C 68 ASP cc_start: 0.7571 (t0) cc_final: 0.7299 (t0) REVERT: C 97 GLU cc_start: 0.6959 (tp30) cc_final: 0.6533 (tp30) REVERT: C 288 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8083 (ttpp) outliers start: 62 outliers final: 25 residues processed: 183 average time/residue: 1.2550 time to fit residues: 252.1466 Evaluate side-chains 153 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 166 ARG 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 386 LYS Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.0980 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 380 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13862 Z= 0.202 Angle : 0.528 7.020 18704 Z= 0.272 Chirality : 0.043 0.184 2087 Planarity : 0.003 0.039 2388 Dihedral : 6.994 134.447 1813 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.87 % Allowed : 18.33 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1653 helix: 0.60 (0.21), residues: 630 sheet: -1.32 (0.25), residues: 385 loop : -1.04 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 242 HIS 0.003 0.001 HIS B 463 PHE 0.016 0.001 PHE A 104 TYR 0.015 0.001 TYR B 504 ARG 0.002 0.000 ARG A 174 *********************** 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 fitting. rotamer outliers: 58 poor density : 135 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 166 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6207 (tpm-80) REVERT: A 188 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8156 (ttpt) REVERT: A 339 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8731 (tt) REVERT: B 427 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: B 548 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7576 (tppt) REVERT: B 559 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: C 68 ASP cc_start: 0.7564 (t0) cc_final: 0.7290 (t0) REVERT: C 97 GLU cc_start: 0.6990 (tp30) cc_final: 0.6664 (tp30) REVERT: C 144 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7987 (mmtt) REVERT: C 288 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8064 (ttpp) outliers start: 58 outliers final: 32 residues processed: 181 average time/residue: 1.3565 time to fit residues: 268.3149 Evaluate side-chains 161 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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 297 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 14 GLN B 381 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4964 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= 0.160 Angle : 0.509 7.260 18704 Z= 0.262 Chirality : 0.043 0.169 2087 Planarity : 0.003 0.039 2388 Dihedral : 6.912 135.763 1813 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.07 % Allowed : 18.87 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1653 helix: 0.76 (0.21), residues: 633 sheet: -1.24 (0.26), residues: 385 loop : -0.92 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 242 HIS 0.003 0.001 HIS C 309 PHE 0.014 0.001 PHE A 104 TYR 0.013 0.001 TYR B 504 ARG 0.007 0.000 ARG A 666 *********************** 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 192 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 188 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8129 (ttpt) REVERT: A 314 ARG cc_start: 0.8106 (mpp80) cc_final: 0.7769 (mpp-170) REVERT: A 339 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 430 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: B 427 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: B 503 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7051 (tp30) REVERT: B 548 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7578 (mtmm) REVERT: B 559 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: C 108 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6209 (mm-40) REVERT: C 144 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7940 (mmtt) REVERT: C 288 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: D 256 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7100 (mm-30) outliers start: 46 outliers final: 21 residues processed: 182 average time/residue: 1.2692 time to fit residues: 252.8581 Evaluate side-chains 152 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 108 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 386 LYS Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 280 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 153 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 159 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 381 GLN B 381 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13862 Z= 0.152 Angle : 0.512 8.501 18704 Z= 0.264 Chirality : 0.042 0.165 2087 Planarity : 0.003 0.039 2388 Dihedral : 6.876 136.289 1813 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.40 % Allowed : 19.00 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1653 helix: 0.84 (0.21), residues: 633 sheet: -1.17 (0.26), residues: 383 loop : -0.88 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 148 HIS 0.003 0.001 HIS C 309 PHE 0.014 0.001 PHE A 104 TYR 0.013 0.001 TYR B 203 ARG 0.007 0.000 ARG A 666 *********************** 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 187 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 136 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 188 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: A 314 ARG cc_start: 0.8089 (mpp80) cc_final: 0.7797 (mpp-170) REVERT: A 339 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8714 (tt) REVERT: A 430 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: B 427 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: B 503 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7050 (tp30) REVERT: B 548 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7562 (mtmm) REVERT: B 559 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 144 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.7929 (mmtt) REVERT: D 256 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7091 (mm-30) outliers start: 51 outliers final: 23 residues processed: 174 average time/residue: 1.2413 time to fit residues: 239.5711 Evaluate side-chains 154 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 108 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 386 LYS 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 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 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 280 LYS 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 63 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 336 ASN A 381 GLN B 381 GLN B 463 HIS B 631 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13862 Z= 0.257 Angle : 0.554 8.530 18704 Z= 0.285 Chirality : 0.044 0.179 2087 Planarity : 0.004 0.040 2388 Dihedral : 7.072 137.029 1813 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.33 % Allowed : 19.33 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1653 helix: 0.76 (0.21), residues: 631 sheet: -1.17 (0.26), residues: 385 loop : -0.89 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 148 HIS 0.004 0.001 HIS A 463 PHE 0.014 0.001 PHE D 261 TYR 0.022 0.002 TYR C 23 ARG 0.008 0.000 ARG A 666 *********************** 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 175 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8196 (ttpt) REVERT: A 314 ARG cc_start: 0.8127 (mpp80) cc_final: 0.7849 (mpp-170) REVERT: A 339 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 427 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: B 503 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7072 (tp30) REVERT: B 559 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: C 68 ASP cc_start: 0.7487 (t0) cc_final: 0.7160 (t0) REVERT: C 144 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8038 (mmtt) REVERT: D 256 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7154 (mm-30) outliers start: 50 outliers final: 29 residues processed: 163 average time/residue: 1.1138 time to fit residues: 201.2693 Evaluate side-chains 150 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 108 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 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 386 LYS 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 594 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 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 63 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 D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 0.0050 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN B 55 GLN B 381 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13862 Z= 0.165 Angle : 0.513 7.570 18704 Z= 0.265 Chirality : 0.043 0.168 2087 Planarity : 0.003 0.040 2388 Dihedral : 6.938 135.514 1813 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.53 % Allowed : 20.27 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1653 helix: 0.85 (0.21), residues: 633 sheet: -1.14 (0.27), residues: 373 loop : -0.78 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 9 HIS 0.004 0.001 HIS B 463 PHE 0.013 0.001 PHE B 6 TYR 0.020 0.001 TYR C 23 ARG 0.007 0.000 ARG A 666 *********************** 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 168 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 188 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8175 (ttpt) REVERT: A 314 ARG cc_start: 0.8047 (mpp80) cc_final: 0.7785 (mpp-170) REVERT: A 339 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8712 (tt) REVERT: A 430 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: B 427 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: B 503 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7023 (tp30) REVERT: B 548 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7674 (mtmm) REVERT: B 559 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: C 68 ASP cc_start: 0.7405 (t0) cc_final: 0.7068 (t0) REVERT: C 144 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8003 (mmtt) REVERT: C 238 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7818 (ttt90) REVERT: D 256 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7115 (mm-30) outliers start: 38 outliers final: 22 residues processed: 160 average time/residue: 1.2089 time to fit residues: 213.0580 Evaluate side-chains 149 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 108 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 386 LYS 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 594 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 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 382 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 463 HIS B 578 GLN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 13862 Z= 0.397 Angle : 0.644 10.413 18704 Z= 0.330 Chirality : 0.047 0.173 2087 Planarity : 0.004 0.044 2388 Dihedral : 7.322 140.931 1813 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1653 helix: 0.58 (0.21), residues: 633 sheet: -1.27 (0.26), residues: 374 loop : -0.86 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 9 HIS 0.006 0.001 HIS A 463 PHE 0.018 0.002 PHE D 261 TYR 0.019 0.002 TYR C 23 ARG 0.007 0.001 ARG A 666 ********************** 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 155 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 188 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: A 314 ARG cc_start: 0.8141 (mpp80) cc_final: 0.7864 (mpp-170) REVERT: A 339 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8789 (tt) REVERT: B 427 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: B 503 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7053 (tp30) REVERT: B 548 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7738 (mtmm) REVERT: C 68 ASP cc_start: 0.7575 (t0) cc_final: 0.7278 (t0) REVERT: C 144 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8033 (mmtt) REVERT: D 256 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7233 (mm-30) outliers start: 36 outliers final: 22 residues processed: 146 average time/residue: 1.2000 time to fit residues: 193.9444 Evaluate side-chains 137 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 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 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN B 382 ASN B 463 HIS C 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103175 restraints weight = 21624.238| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.77 r_work: 0.3221 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13862 Z= 0.200 Angle : 0.569 10.568 18704 Z= 0.291 Chirality : 0.044 0.172 2087 Planarity : 0.004 0.040 2388 Dihedral : 7.127 134.972 1813 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.87 % Allowed : 21.60 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1653 helix: 0.71 (0.21), residues: 634 sheet: -1.27 (0.26), residues: 373 loop : -0.78 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 9 HIS 0.003 0.001 HIS B 463 PHE 0.033 0.001 PHE B 579 TYR 0.020 0.001 TYR C 23 ARG 0.010 0.000 ARG A 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5282.53 seconds wall clock time: 93 minutes 13.88 seconds (5593.88 seconds total)