Starting phenix.real_space_refine on Fri Oct 23 18:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25jx_80170/10_2026/25jx_80170.cif Found real_map, /net/cci-nas-00/data/ceres_data/25jx_80170/10_2026/25jx_80170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25jx_80170/10_2026/25jx_80170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25jx_80170/10_2026/25jx_80170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25jx_80170/10_2026/25jx_80170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25jx_80170/10_2026/25jx_80170.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.238 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6959 2.51 5 N 1695 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10611 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5270 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5380 Chain: "B" Number of atoms: 5273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5376 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.96, per 1000 atoms: 0.37 Number of scatterers: 10611 At special positions: 0 Unit cell: (123.889, 89.4159, 107.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 60 16.00 P 4 15.00 O 1891 8.00 N 1695 7.00 C 6959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 860.7 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 3 sheets defined 67.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.738A pdb=" N MET A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.571A pdb=" N THR A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 76 " --> pdb=" O ILE A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.502A pdb=" N GLY A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.513A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.695A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.991A pdb=" N LYS A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.998A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.551A pdb=" N VAL A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.661A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 4.200A pdb=" N VAL A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 322 through 349 removed outlier: 3.530A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 402 removed outlier: 3.532A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 440 removed outlier: 4.210A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 removed outlier: 4.019A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 3.590A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 537 removed outlier: 3.899A pdb=" N VAL A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.650A pdb=" N ILE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 582 removed outlier: 4.278A pdb=" N SER A 575 " --> pdb=" O THR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.730A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 744 through 753 Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.553A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.662A pdb=" N LEU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.573A pdb=" N THR B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 76 " --> pdb=" O ILE B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 76' Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.510A pdb=" N GLY B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.513A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.622A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 4.015A pdb=" N LYS B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.993A pdb=" N SER B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.570A pdb=" N VAL B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.659A pdb=" N PHE B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 4.202A pdb=" N VAL B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 322 through 349 removed outlier: 3.530A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Proline residue: B 336 - end of helix Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 368 through 402 removed outlier: 3.519A pdb=" N THR B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 removed outlier: 4.166A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 472 removed outlier: 3.891A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 500 removed outlier: 3.532A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 537 removed outlier: 4.425A pdb=" N LEU B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.638A pdb=" N ILE B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 removed outlier: 4.266A pdb=" N SER B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 653 removed outlier: 3.733A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 744 through 753 Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.563A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 611 removed outlier: 7.921A pdb=" N PHE A 620 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 588 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N CYS A 622 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 590 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 624 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER A 592 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N TYR A 626 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 594 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER A 583 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 556 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS A 585 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY A 558 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 729 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 559 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 731 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 561 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY A 733 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N TYR A 563 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N THR A 735 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU A 777 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR A 783 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 785 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 738 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU B 777 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 730 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL B 779 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET B 732 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N MET B 781 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU B 734 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TYR B 783 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B 736 " --> pdb=" O TYR B 783 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 785 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 738 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 729 " --> pdb=" O PRO B 557 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 559 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU B 731 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 561 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY B 733 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N TYR B 563 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N THR B 735 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B 583 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 556 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS B 585 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY B 558 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE B 620 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 411 554 hydrogen bonds defined for protein. 1589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1604 1.31 - 1.44: 3045 1.44 - 1.56: 6091 1.56 - 1.68: 6 1.68 - 1.81: 104 Bond restraints: 10850 Sorted by residual: bond pdb=" CA ALA A 140 " pdb=" CB ALA A 140 " ideal model delta sigma weight residual 1.530 1.464 0.067 1.50e-02 4.44e+03 2.00e+01 bond pdb=" C VAL A 457 " pdb=" O VAL A 457 " ideal model delta sigma weight residual 1.236 1.189 0.048 1.19e-02 7.06e+03 1.60e+01 bond pdb=" C VAL B 457 " pdb=" O VAL B 457 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.19e-02 7.06e+03 1.50e+01 bond pdb=" N ASP A 631 " pdb=" CA ASP A 631 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" C THR B 456 " pdb=" O THR B 456 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.16e-02 7.43e+03 1.13e+01 ... (remaining 10845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 14404 2.72 - 5.44: 270 5.44 - 8.15: 53 8.15 - 10.87: 10 10.87 - 13.59: 2 Bond angle restraints: 14739 Sorted by residual: angle pdb=" N VAL A 459 " pdb=" CA VAL A 459 " pdb=" C VAL A 459 " ideal model delta sigma weight residual 112.35 100.36 11.99 1.41e+00 5.03e-01 7.23e+01 angle pdb=" N ALA A 231 " pdb=" CA ALA A 231 " pdb=" C ALA A 231 " ideal model delta sigma weight residual 114.75 104.53 10.22 1.26e+00 6.30e-01 6.58e+01 angle pdb=" N ALA B 231 " pdb=" CA ALA B 231 " pdb=" C ALA B 231 " ideal model delta sigma weight residual 114.75 104.55 10.20 1.26e+00 6.30e-01 6.56e+01 angle pdb=" N MET B 519 " pdb=" CA MET B 519 " pdb=" C MET B 519 " ideal model delta sigma weight residual 114.62 105.56 9.06 1.14e+00 7.69e-01 6.32e+01 angle pdb=" CA PHE B 440 " pdb=" CB PHE B 440 " pdb=" CG PHE B 440 " ideal model delta sigma weight residual 113.80 121.48 -7.68 1.00e+00 1.00e+00 5.90e+01 ... (remaining 14734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 5907 25.00 - 49.99: 390 49.99 - 74.99: 47 74.99 - 99.98: 6 99.98 - 124.98: 1 Dihedral angle restraints: 6351 sinusoidal: 2466 harmonic: 3885 Sorted by residual: dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 64.97 -124.98 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" CD ARG A 292 " pdb=" NE ARG A 292 " pdb=" CZ ARG A 292 " pdb=" NH1 ARG A 292 " ideal model delta sinusoidal sigma weight residual 0.00 -48.61 48.61 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CA ILE B 512 " pdb=" C ILE B 512 " pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 6348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1514 0.070 - 0.141: 191 0.141 - 0.211: 15 0.211 - 0.281: 5 0.281 - 0.352: 3 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA VAL A 459 " pdb=" N VAL A 459 " pdb=" C VAL A 459 " pdb=" CB VAL A 459 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB VAL A 457 " pdb=" CA VAL A 457 " pdb=" CG1 VAL A 457 " pdb=" CG2 VAL A 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA LYS B 474 " pdb=" N LYS B 474 " pdb=" C LYS B 474 " pdb=" CB LYS B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 1725 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 292 " -0.862 9.50e-02 1.11e+02 3.86e-01 9.06e+01 pdb=" NE ARG A 292 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 292 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 292 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 292 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 458 " -0.024 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C MET B 458 " 0.086 2.00e-02 2.50e+03 pdb=" O MET B 458 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL B 459 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 291 " 0.021 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C ARG A 291 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG A 291 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 292 " 0.024 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 1073 2.74 - 3.34: 11957 3.34 - 3.94: 20227 3.94 - 4.54: 29968 4.54 - 5.14: 45489 Nonbonded interactions: 108714 Sorted by model distance: nonbonded pdb=" OE1 GLU A 534 " pdb=" O HOH A1001 " model vdw 2.138 3.040 nonbonded pdb=" O TYR A 289 " pdb=" OG1 THR A 293 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR B 104 " pdb=" O LEU B 281 " model vdw 2.205 3.040 nonbonded pdb=" O PRO A 336 " pdb=" OG1 THR A 340 " model vdw 2.207 3.040 nonbonded pdb=" O PRO B 336 " pdb=" OG1 THR B 340 " model vdw 2.208 3.040 ... (remaining 108709 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 55 through 138 or resid 140 through 529 or resid 531 throu \ gh 902)) selection = (chain 'B' and (resid 55 through 138 or resid 140 through 529 or resid 531 throu \ gh 902)) } 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=0.50 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: 1.530 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.270 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.005 0.067 10850 Z= 0.275 Angle : 0.914 13.590 14739 Z= 0.551 Chirality : 0.051 0.352 1728 Planarity : 0.011 0.386 1787 Dihedral : 16.127 124.977 3867 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.29 % Favored : 92.17 % Rotamer: Outliers : 3.71 % Allowed : 18.22 % Favored : 78.07 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.19), residues: 1318 helix: -2.46 (0.15), residues: 834 sheet: -1.42 (0.47), residues: 106 loop : -3.11 (0.27), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 292 TYR 0.014 0.002 TYR A 354 PHE 0.014 0.002 PHE A 130 TRP 0.016 0.002 TRP B 473 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.28 (10850) covalent geometry : angle 0.91427 / 0.55 (14739) hydrogen bonds : bond 0.16649 / 11.20 ( 554) hydrogen bonds : angle 7.66825 / 5.48 ( 1589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.479 Fit side-chains REVERT: A 93 ASP cc_start: 0.7160 (t70) cc_final: 0.6819 (t0) REVERT: A 142 MET cc_start: 0.8225 (mmm) cc_final: 0.7511 (mmm) REVERT: A 168 ARG cc_start: 0.5019 (OUTLIER) cc_final: 0.4688 (tpm-80) REVERT: A 179 ASN cc_start: 0.7170 (m110) cc_final: 0.6854 (p0) REVERT: A 239 PHE cc_start: 0.7763 (m-80) cc_final: 0.7554 (m-80) REVERT: A 474 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5104 (mttt) REVERT: A 499 MET cc_start: 0.7543 (tpt) cc_final: 0.7330 (mmm) REVERT: A 534 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 93 ASP cc_start: 0.7153 (t70) cc_final: 0.6842 (t0) REVERT: B 168 ARG cc_start: 0.5035 (OUTLIER) cc_final: 0.4603 (tmm160) REVERT: B 179 ASN cc_start: 0.7182 (m110) cc_final: 0.6887 (p0) REVERT: B 239 PHE cc_start: 0.7757 (m-80) cc_final: 0.7555 (m-80) REVERT: B 295 ARG cc_start: 0.6383 (mmt180) cc_final: 0.5031 (ttt-90) REVERT: B 317 ASP cc_start: 0.7802 (m-30) cc_final: 0.7521 (m-30) REVERT: B 499 MET cc_start: 0.7562 (tpt) cc_final: 0.7333 (mmm) REVERT: B 634 GLU cc_start: 0.7344 (pp20) cc_final: 0.6818 (pp20) outliers start: 43 outliers final: 24 residues processed: 222 average time/residue: 0.5672 time to fit residues: 135.1309 Evaluate side-chains 180 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 744 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 273 HIS A 385 GLN A 476 ASN A 568 ASN A 651 HIS A 652 HIS B 179 ASN B 223 ASN B 273 HIS B 385 GLN B 448 HIS B 476 ASN B 568 ASN B 651 HIS B 652 HIS B 654 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129960 restraints weight = 15297.939| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.00 r_work: 0.3289 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10850 Z= 0.206 Angle : 0.729 10.394 14739 Z= 0.377 Chirality : 0.047 0.174 1728 Planarity : 0.005 0.035 1787 Dihedral : 9.109 128.722 1519 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.22 % Favored : 92.55 % Rotamer: Outliers : 4.15 % Allowed : 19.17 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.22), residues: 1318 helix: -1.04 (0.17), residues: 832 sheet: -1.27 (0.48), residues: 106 loop : -2.48 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 241 TYR 0.015 0.002 TYR A 285 PHE 0.018 0.002 PHE B 182 TRP 0.014 0.002 TRP B 473 HIS 0.009 0.002 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (10850) covalent geometry : angle 0.72909 / 0.38 (14739) hydrogen bonds : bond 0.05194 / 3.39 ( 554) hydrogen bonds : angle 5.22736 / 3.67 ( 1589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.316 Fit side-chains REVERT: A 93 ASP cc_start: 0.7453 (t70) cc_final: 0.7103 (t0) REVERT: A 142 MET cc_start: 0.8293 (mmm) cc_final: 0.7776 (mmm) REVERT: A 151 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6172 (pm20) REVERT: A 179 ASN cc_start: 0.6859 (m110) cc_final: 0.6339 (p0) REVERT: A 239 PHE cc_start: 0.7662 (m-80) cc_final: 0.7431 (m-80) REVERT: A 474 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4255 (mtmt) REVERT: A 499 MET cc_start: 0.8036 (tpt) cc_final: 0.7758 (mmm) REVERT: A 534 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 784 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: B 59 MET cc_start: 0.7601 (mmm) cc_final: 0.7309 (mmt) REVERT: B 93 ASP cc_start: 0.7498 (t70) cc_final: 0.7089 (m-30) REVERT: B 151 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6196 (pm20) REVERT: B 155 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7278 (mt) REVERT: B 179 ASN cc_start: 0.7111 (m-40) cc_final: 0.6665 (p0) REVERT: B 239 PHE cc_start: 0.7648 (m-80) cc_final: 0.7410 (m-80) REVERT: B 295 ARG cc_start: 0.6644 (mmt180) cc_final: 0.4447 (ttt-90) REVERT: B 499 MET cc_start: 0.7889 (tpt) cc_final: 0.7679 (mmm) REVERT: B 541 ARG cc_start: 0.7829 (mtm110) cc_final: 0.5931 (ttm170) REVERT: B 634 GLU cc_start: 0.7491 (pp20) cc_final: 0.6751 (pp20) REVERT: B 784 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7165 (pp20) outliers start: 48 outliers final: 25 residues processed: 191 average time/residue: 0.5583 time to fit residues: 114.6335 Evaluate side-chains 182 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [92, 56, 67, 4, 19, 126, 68, 55, 7, 91, 96] chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 568 ASN A 652 HIS A 654 HIS B 282 ASN B 476 ASN B 568 ASN B 652 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132981 restraints weight = 15252.971| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.01 r_work: 0.3336 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10850 Z= 0.134 Angle : 0.637 9.264 14739 Z= 0.329 Chirality : 0.044 0.180 1728 Planarity : 0.004 0.036 1787 Dihedral : 7.875 128.298 1493 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.08 % Favored : 93.77 % Rotamer: Outliers : 3.37 % Allowed : 20.90 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.23), residues: 1318 helix: -0.37 (0.18), residues: 848 sheet: -1.08 (0.49), residues: 108 loop : -2.10 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 241 TYR 0.012 0.001 TYR A 104 PHE 0.016 0.001 PHE B 182 TRP 0.010 0.002 TRP B 258 HIS 0.006 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10850) covalent geometry : angle 0.63670 / 0.33 (14739) hydrogen bonds : bond 0.04020 / 2.61 ( 554) hydrogen bonds : angle 4.73565 / 3.33 ( 1589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.386 Fit side-chains REVERT: A 59 MET cc_start: 0.7537 (mmm) cc_final: 0.7212 (mmt) REVERT: A 93 ASP cc_start: 0.7416 (t70) cc_final: 0.6990 (m-30) REVERT: A 151 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6131 (pm20) REVERT: A 179 ASN cc_start: 0.6883 (m110) cc_final: 0.6272 (p0) REVERT: A 239 PHE cc_start: 0.7586 (m-80) cc_final: 0.7360 (m-80) REVERT: A 293 THR cc_start: 0.8329 (m) cc_final: 0.7741 (p) REVERT: A 311 THR cc_start: 0.8718 (m) cc_final: 0.8508 (p) REVERT: A 474 LYS cc_start: 0.4891 (OUTLIER) cc_final: 0.3995 (mttt) REVERT: A 499 MET cc_start: 0.8020 (tpt) cc_final: 0.7652 (mmp) REVERT: A 534 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 619 MET cc_start: 0.8702 (mtp) cc_final: 0.8499 (mtp) REVERT: A 784 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: B 59 MET cc_start: 0.7458 (mmm) cc_final: 0.7172 (mmt) REVERT: B 93 ASP cc_start: 0.7540 (t70) cc_final: 0.7140 (m-30) REVERT: B 151 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: B 179 ASN cc_start: 0.7338 (m-40) cc_final: 0.6785 (p0) REVERT: B 239 PHE cc_start: 0.7590 (m-80) cc_final: 0.7359 (m-80) REVERT: B 295 ARG cc_start: 0.6623 (mmt180) cc_final: 0.4407 (ttt-90) REVERT: B 610 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7778 (ttp-110) REVERT: B 784 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7168 (pp20) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 0.5142 time to fit residues: 107.7217 Evaluate side-chains 179 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [39, 22, 93, 84, 35, 64, 53, 86, 99, 49, 107] chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 107 optimal weight: 0.0050 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 476 ASN A 568 ASN A 652 HIS A 654 HIS B 476 ASN B 568 ASN B 652 HIS B 654 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.161511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134406 restraints weight = 15500.491| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.10 r_work: 0.3355 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10850 Z= 0.107 Angle : 0.594 10.584 14739 Z= 0.302 Chirality : 0.042 0.190 1728 Planarity : 0.004 0.038 1787 Dihedral : 7.138 124.839 1483 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 2.94 % Allowed : 21.33 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1318 helix: 0.12 (0.19), residues: 842 sheet: -0.81 (0.51), residues: 106 loop : -1.79 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 241 TYR 0.013 0.001 TYR A 288 PHE 0.014 0.001 PHE B 182 TRP 0.009 0.001 TRP A 258 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (10850) covalent geometry : angle 0.59422 / 0.30 (14739) hydrogen bonds : bond 0.03179 / 2.04 ( 554) hydrogen bonds : angle 4.37265 / 3.07 ( 1589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.319 Fit side-chains REVERT: A 57 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6533 (m) REVERT: A 59 MET cc_start: 0.7364 (mmm) cc_final: 0.7035 (mmt) REVERT: A 93 ASP cc_start: 0.7394 (t70) cc_final: 0.7044 (m-30) REVERT: A 151 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6058 (pm20) REVERT: A 179 ASN cc_start: 0.6656 (m110) cc_final: 0.6140 (p0) REVERT: A 239 PHE cc_start: 0.7572 (m-80) cc_final: 0.7349 (m-80) REVERT: A 311 THR cc_start: 0.8737 (m) cc_final: 0.8514 (p) REVERT: A 417 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6112 (mm-30) REVERT: A 474 LYS cc_start: 0.5062 (OUTLIER) cc_final: 0.4307 (mttp) REVERT: A 499 MET cc_start: 0.7931 (tpt) cc_final: 0.7684 (mmm) REVERT: A 534 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 619 MET cc_start: 0.8602 (mtp) cc_final: 0.8398 (mtp) REVERT: A 640 ARG cc_start: 0.7325 (ttm110) cc_final: 0.7080 (mtm110) REVERT: A 784 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: B 57 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6470 (m) REVERT: B 59 MET cc_start: 0.7362 (mmm) cc_final: 0.7095 (mmt) REVERT: B 93 ASP cc_start: 0.7499 (t70) cc_final: 0.7077 (m-30) REVERT: B 151 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5959 (pm20) REVERT: B 179 ASN cc_start: 0.7481 (m-40) cc_final: 0.6789 (p0) REVERT: B 239 PHE cc_start: 0.7563 (m-80) cc_final: 0.7326 (m-80) REVERT: B 295 ARG cc_start: 0.6423 (mmt180) cc_final: 0.4299 (ttt-90) REVERT: B 311 THR cc_start: 0.8738 (m) cc_final: 0.8499 (p) REVERT: B 417 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: B 499 MET cc_start: 0.7707 (mmm) cc_final: 0.5513 (ptt) REVERT: B 610 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7775 (ttp-110) REVERT: B 619 MET cc_start: 0.8659 (mtp) cc_final: 0.8404 (mtp) REVERT: B 634 GLU cc_start: 0.7354 (pp20) cc_final: 0.6617 (pp20) REVERT: B 640 ARG cc_start: 0.7373 (ttm110) cc_final: 0.7168 (mtm110) REVERT: B 784 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6790 (pp20) outliers start: 34 outliers final: 10 residues processed: 211 average time/residue: 0.4732 time to fit residues: 108.9687 Evaluate side-chains 188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 564 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [20, 104, 128, 26, 125, 44, 35, 93, 22, 40, 57] chunk 20 optimal weight: 0.1980 chunk 104 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 ASN A 652 HIS A 654 HIS B 568 ASN B 652 HIS B 654 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132652 restraints weight = 19382.215| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.43 r_work: 0.3342 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10850 Z= 0.108 Angle : 0.586 10.143 14739 Z= 0.298 Chirality : 0.042 0.184 1728 Planarity : 0.004 0.040 1787 Dihedral : 7.009 122.154 1483 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 3.37 % Allowed : 21.85 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1318 helix: 0.39 (0.19), residues: 842 sheet: -0.69 (0.51), residues: 106 loop : -1.52 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 TYR 0.013 0.001 TYR A 288 PHE 0.023 0.001 PHE A 182 TRP 0.009 0.001 TRP B 258 HIS 0.003 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (10850) covalent geometry : angle 0.58552 / 0.30 (14739) hydrogen bonds : bond 0.03226 / 2.09 ( 554) hydrogen bonds : angle 4.26970 / 2.99 ( 1589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.316 Fit side-chains REVERT: A 57 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.6459 (m) REVERT: A 59 MET cc_start: 0.7154 (mmm) cc_final: 0.6843 (mmt) REVERT: A 93 ASP cc_start: 0.7270 (t70) cc_final: 0.6893 (m-30) REVERT: A 151 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6126 (pm20) REVERT: A 179 ASN cc_start: 0.6721 (m110) cc_final: 0.6133 (p0) REVERT: A 232 ILE cc_start: 0.7430 (mt) cc_final: 0.7164 (mp) REVERT: A 239 PHE cc_start: 0.7495 (m-80) cc_final: 0.7243 (m-80) REVERT: A 241 ARG cc_start: 0.7762 (ptp-110) cc_final: 0.7415 (ptm-80) REVERT: A 311 THR cc_start: 0.8686 (m) cc_final: 0.8444 (p) REVERT: A 387 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7305 (mmm) REVERT: A 417 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6081 (mm-30) REVERT: A 474 LYS cc_start: 0.4714 (OUTLIER) cc_final: 0.4193 (mttp) REVERT: A 499 MET cc_start: 0.7815 (tpt) cc_final: 0.7466 (mmp) REVERT: A 534 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 575 SER cc_start: 0.8306 (t) cc_final: 0.7896 (p) REVERT: A 619 MET cc_start: 0.8429 (mtp) cc_final: 0.8155 (mtp) REVERT: A 640 ARG cc_start: 0.7141 (ttm110) cc_final: 0.6893 (mtm110) REVERT: A 784 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7061 (pp20) REVERT: B 57 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6437 (m) REVERT: B 59 MET cc_start: 0.7219 (mmm) cc_final: 0.6968 (mmt) REVERT: B 93 ASP cc_start: 0.7386 (t70) cc_final: 0.7002 (m-30) REVERT: B 119 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 151 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6116 (pm20) REVERT: B 179 ASN cc_start: 0.7448 (m-40) cc_final: 0.6786 (p0) REVERT: B 239 PHE cc_start: 0.7511 (m-80) cc_final: 0.7298 (m-80) REVERT: B 241 ARG cc_start: 0.7797 (ptp-110) cc_final: 0.7447 (ptm-80) REVERT: B 295 ARG cc_start: 0.6347 (mmt180) cc_final: 0.4249 (ttt-90) REVERT: B 311 THR cc_start: 0.8684 (m) cc_final: 0.8461 (p) REVERT: B 417 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6000 (mm-30) REVERT: B 610 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7687 (ttp-110) REVERT: B 619 MET cc_start: 0.8479 (mtp) cc_final: 0.8195 (mtp) REVERT: B 634 GLU cc_start: 0.7282 (pp20) cc_final: 0.6507 (pp20) REVERT: B 640 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6925 (mtm110) REVERT: B 784 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6721 (pp20) outliers start: 39 outliers final: 18 residues processed: 208 average time/residue: 0.4629 time to fit residues: 105.0423 Evaluate side-chains 200 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [119, 32, 26, 49, 43, 124, 131, 34, 74, 130, 94] chunk 119 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 568 ASN A 652 HIS A 654 HIS B 568 ASN B 652 HIS B 654 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134711 restraints weight = 16812.765| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.21 r_work: 0.3369 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10850 Z= 0.105 Angle : 0.583 11.046 14739 Z= 0.295 Chirality : 0.042 0.190 1728 Planarity : 0.004 0.040 1787 Dihedral : 6.901 120.286 1483 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 3.37 % Allowed : 22.88 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1318 helix: 0.60 (0.19), residues: 836 sheet: -0.57 (0.51), residues: 106 loop : -1.37 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 541 TYR 0.015 0.001 TYR A 288 PHE 0.031 0.001 PHE A 182 TRP 0.009 0.001 TRP B 258 HIS 0.003 0.001 HIS B 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (10850) covalent geometry : angle 0.58288 / 0.29 (14739) hydrogen bonds : bond 0.03126 / 2.02 ( 554) hydrogen bonds : angle 4.20598 / 2.94 ( 1589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.400 Fit side-chains REVERT: A 57 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6590 (m) REVERT: A 93 ASP cc_start: 0.7483 (t70) cc_final: 0.7097 (m-30) REVERT: A 119 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7425 (mp) REVERT: A 151 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6192 (pm20) REVERT: A 179 ASN cc_start: 0.6767 (m110) cc_final: 0.6147 (p0) REVERT: A 239 PHE cc_start: 0.7580 (m-80) cc_final: 0.7344 (m-80) REVERT: A 241 ARG cc_start: 0.7958 (ptp-110) cc_final: 0.7645 (ptm-80) REVERT: A 260 THR cc_start: 0.8007 (m) cc_final: 0.7712 (t) REVERT: A 311 THR cc_start: 0.8743 (m) cc_final: 0.8509 (p) REVERT: A 417 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: A 474 LYS cc_start: 0.4804 (OUTLIER) cc_final: 0.4162 (mttp) REVERT: A 499 MET cc_start: 0.7917 (tpt) cc_final: 0.7598 (mmp) REVERT: A 534 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 575 SER cc_start: 0.8406 (t) cc_final: 0.8029 (p) REVERT: A 619 MET cc_start: 0.8494 (mtp) cc_final: 0.8268 (mtp) REVERT: A 640 ARG cc_start: 0.7274 (ttm110) cc_final: 0.7022 (mtm110) REVERT: A 784 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7097 (pp20) REVERT: B 57 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6497 (m) REVERT: B 93 ASP cc_start: 0.7584 (t70) cc_final: 0.7193 (m-30) REVERT: B 119 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7497 (mp) REVERT: B 151 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5979 (pm20) REVERT: B 179 ASN cc_start: 0.7421 (m-40) cc_final: 0.6854 (p0) REVERT: B 239 PHE cc_start: 0.7608 (m-80) cc_final: 0.7356 (m-80) REVERT: B 241 ARG cc_start: 0.7923 (ptp-110) cc_final: 0.7610 (ptm-80) REVERT: B 260 THR cc_start: 0.8010 (m) cc_final: 0.7714 (t) REVERT: B 295 ARG cc_start: 0.6315 (mmt180) cc_final: 0.4191 (ttt-90) REVERT: B 311 THR cc_start: 0.8744 (m) cc_final: 0.8501 (p) REVERT: B 357 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8414 (m) REVERT: B 417 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6034 (mm-30) REVERT: B 499 MET cc_start: 0.7734 (mmm) cc_final: 0.5593 (ptt) REVERT: B 610 ARG cc_start: 0.8245 (ttp-170) cc_final: 0.7849 (ttp-110) REVERT: B 619 MET cc_start: 0.8513 (mtp) cc_final: 0.8263 (mtp) REVERT: B 640 ARG cc_start: 0.7382 (ttm110) cc_final: 0.7133 (mtm110) REVERT: B 784 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6757 (pp20) outliers start: 39 outliers final: 16 residues processed: 202 average time/residue: 0.4827 time to fit residues: 106.1925 Evaluate side-chains 196 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [27, 112, 16, 71, 128, 74, 43, 86, 50, 29, 80] chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 ASN A 652 HIS A 654 HIS B 476 ASN B 568 ASN B 652 HIS B 654 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130836 restraints weight = 16137.281| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.15 r_work: 0.3331 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10850 Z= 0.116 Angle : 0.595 9.618 14739 Z= 0.301 Chirality : 0.043 0.199 1728 Planarity : 0.004 0.039 1787 Dihedral : 6.894 119.470 1482 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 3.54 % Allowed : 22.88 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1318 helix: 0.63 (0.19), residues: 836 sheet: -0.59 (0.51), residues: 106 loop : -1.35 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 292 TYR 0.015 0.001 TYR A 288 PHE 0.012 0.001 PHE A 182 TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS B 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10850) covalent geometry : angle 0.59468 / 0.30 (14739) hydrogen bonds : bond 0.03420 / 2.22 ( 554) hydrogen bonds : angle 4.27149 / 2.98 ( 1589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.347 Fit side-chains REVERT: A 57 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6441 (m) REVERT: A 93 ASP cc_start: 0.7462 (t70) cc_final: 0.7053 (m-30) REVERT: A 119 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 151 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6220 (pm20) REVERT: A 179 ASN cc_start: 0.6721 (m110) cc_final: 0.6100 (p0) REVERT: A 239 PHE cc_start: 0.7576 (m-80) cc_final: 0.7342 (m-80) REVERT: A 241 ARG cc_start: 0.7953 (ptp-110) cc_final: 0.7657 (ptm-80) REVERT: A 260 THR cc_start: 0.7968 (m) cc_final: 0.7649 (t) REVERT: A 293 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7699 (p) REVERT: A 311 THR cc_start: 0.8758 (m) cc_final: 0.8525 (p) REVERT: A 417 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6155 (mm-30) REVERT: A 474 LYS cc_start: 0.4514 (OUTLIER) cc_final: 0.3879 (mttp) REVERT: A 499 MET cc_start: 0.7869 (tpt) cc_final: 0.7541 (mmp) REVERT: A 534 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 575 SER cc_start: 0.8344 (t) cc_final: 0.7980 (p) REVERT: A 619 MET cc_start: 0.8516 (mtp) cc_final: 0.8285 (mtp) REVERT: A 640 ARG cc_start: 0.7295 (ttm110) cc_final: 0.7029 (mtm110) REVERT: A 784 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7078 (pp20) REVERT: B 57 THR cc_start: 0.6704 (OUTLIER) cc_final: 0.6440 (m) REVERT: B 93 ASP cc_start: 0.7537 (t70) cc_final: 0.7171 (m-30) REVERT: B 119 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 151 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5895 (pm20) REVERT: B 179 ASN cc_start: 0.7397 (m-40) cc_final: 0.6813 (p0) REVERT: B 239 PHE cc_start: 0.7589 (m-80) cc_final: 0.7327 (m-80) REVERT: B 241 ARG cc_start: 0.7922 (ptp-110) cc_final: 0.7621 (ptm-80) REVERT: B 260 THR cc_start: 0.7993 (m) cc_final: 0.7680 (t) REVERT: B 295 ARG cc_start: 0.6270 (mmt180) cc_final: 0.4144 (ttt-90) REVERT: B 357 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8344 (m) REVERT: B 417 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: B 499 MET cc_start: 0.7692 (mmm) cc_final: 0.5531 (ptt) REVERT: B 610 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7831 (ttp-110) REVERT: B 619 MET cc_start: 0.8448 (mtp) cc_final: 0.8189 (mtp) REVERT: B 640 ARG cc_start: 0.7330 (ttm110) cc_final: 0.7081 (mtm110) REVERT: B 784 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6728 (pp20) outliers start: 41 outliers final: 18 residues processed: 203 average time/residue: 0.4723 time to fit residues: 104.1532 Evaluate side-chains 196 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [17, 47, 100, 63, 7, 43, 5, 38, 19, 72, 95] chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 ASN A 652 HIS B 568 ASN B 652 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.157094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129479 restraints weight = 18854.535| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.28 r_work: 0.3291 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10850 Z= 0.178 Angle : 0.674 9.937 14739 Z= 0.342 Chirality : 0.046 0.187 1728 Planarity : 0.004 0.037 1787 Dihedral : 7.276 123.580 1482 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.24 % Rotamer: Outliers : 3.28 % Allowed : 23.14 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.24), residues: 1318 helix: 0.34 (0.19), residues: 842 sheet: -0.78 (0.50), residues: 108 loop : -1.42 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 600 TYR 0.021 0.002 TYR A 285 PHE 0.039 0.002 PHE A 182 TRP 0.010 0.002 TRP A 258 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (10850) covalent geometry : angle 0.67439 / 0.34 (14739) hydrogen bonds : bond 0.04472 / 2.92 ( 554) hydrogen bonds : angle 4.61839 / 3.22 ( 1589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.339 Fit side-chains REVERT: A 93 ASP cc_start: 0.7376 (t70) cc_final: 0.6917 (m-30) REVERT: A 119 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 151 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: A 179 ASN cc_start: 0.6783 (m110) cc_final: 0.6177 (p0) REVERT: A 239 PHE cc_start: 0.7592 (m-80) cc_final: 0.7371 (m-80) REVERT: A 241 ARG cc_start: 0.7975 (ptp-110) cc_final: 0.7687 (ptm-80) REVERT: A 417 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: A 474 LYS cc_start: 0.4528 (OUTLIER) cc_final: 0.3795 (mttt) REVERT: A 499 MET cc_start: 0.7831 (tpt) cc_final: 0.7508 (mmm) REVERT: A 534 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 581 LEU cc_start: 0.8110 (mm) cc_final: 0.7813 (mt) REVERT: A 619 MET cc_start: 0.8612 (mtp) cc_final: 0.8390 (mtp) REVERT: A 784 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: B 93 ASP cc_start: 0.7323 (t70) cc_final: 0.6948 (m-30) REVERT: B 119 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7454 (mp) REVERT: B 151 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6240 (pm20) REVERT: B 174 LYS cc_start: 0.7319 (tttp) cc_final: 0.6935 (tmtm) REVERT: B 179 ASN cc_start: 0.7189 (m-40) cc_final: 0.6895 (p0) REVERT: B 239 PHE cc_start: 0.7644 (m-80) cc_final: 0.7423 (m-80) REVERT: B 241 ARG cc_start: 0.7957 (ptp-110) cc_final: 0.7651 (ptm-80) REVERT: B 295 ARG cc_start: 0.6434 (mmt180) cc_final: 0.4366 (ttt-90) REVERT: B 417 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6161 (mm-30) REVERT: B 499 MET cc_start: 0.7723 (mmm) cc_final: 0.5744 (ptt) REVERT: B 619 MET cc_start: 0.8599 (mtp) cc_final: 0.8311 (mtp) REVERT: B 784 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6840 (pp20) outliers start: 38 outliers final: 22 residues processed: 196 average time/residue: 0.4787 time to fit residues: 101.8916 Evaluate side-chains 197 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [51, 114, 92, 118, 19, 88, 94, 6, 25, 96, 52] chunk 51 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 568 ASN A 652 HIS A 654 HIS B 568 ASN B 652 HIS B 654 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136518 restraints weight = 15201.694| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.91 r_work: 0.3408 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10850 Z= 0.126 Angle : 0.610 9.226 14739 Z= 0.311 Chirality : 0.044 0.198 1728 Planarity : 0.004 0.037 1787 Dihedral : 7.085 120.635 1482 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 3.71 % Allowed : 22.97 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.24), residues: 1318 helix: 0.51 (0.19), residues: 840 sheet: -0.61 (0.51), residues: 106 loop : -1.40 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 606 TYR 0.017 0.001 TYR A 288 PHE 0.035 0.001 PHE B 182 TRP 0.013 0.002 TRP A 258 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10850) covalent geometry : angle 0.61013 / 0.31 (14739) hydrogen bonds : bond 0.03624 / 2.36 ( 554) hydrogen bonds : angle 4.43974 / 3.10 ( 1589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.267 Fit side-chains REVERT: A 91 ASP cc_start: 0.6614 (t0) cc_final: 0.6182 (t0) REVERT: A 93 ASP cc_start: 0.7422 (t70) cc_final: 0.7018 (m-30) REVERT: A 119 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7461 (mp) REVERT: A 151 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: A 179 ASN cc_start: 0.6796 (m110) cc_final: 0.6182 (p0) REVERT: A 239 PHE cc_start: 0.7586 (m-80) cc_final: 0.7316 (m-80) REVERT: A 241 ARG cc_start: 0.7953 (ptp-110) cc_final: 0.7667 (ptm-80) REVERT: A 292 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7458 (mtp-110) REVERT: A 293 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7799 (p) REVERT: A 417 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6136 (mm-30) REVERT: A 474 LYS cc_start: 0.4530 (OUTLIER) cc_final: 0.3802 (mttp) REVERT: A 499 MET cc_start: 0.7900 (tpt) cc_final: 0.7577 (mmm) REVERT: A 534 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7192 (mt-10) REVERT: A 575 SER cc_start: 0.8324 (t) cc_final: 0.7987 (p) REVERT: A 581 LEU cc_start: 0.8119 (mm) cc_final: 0.7844 (mt) REVERT: A 619 MET cc_start: 0.8658 (mtp) cc_final: 0.8403 (mtp) REVERT: A 640 ARG cc_start: 0.7293 (mtm110) cc_final: 0.6934 (mtm110) REVERT: A 784 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: B 93 ASP cc_start: 0.7400 (t70) cc_final: 0.6915 (m-30) REVERT: B 119 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7462 (mp) REVERT: B 151 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: B 174 LYS cc_start: 0.7339 (tttp) cc_final: 0.6964 (tmtm) REVERT: B 179 ASN cc_start: 0.7188 (m-40) cc_final: 0.6900 (p0) REVERT: B 239 PHE cc_start: 0.7643 (m-80) cc_final: 0.7418 (m-80) REVERT: B 241 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7797 (ptm-80) REVERT: B 292 ARG cc_start: 0.7488 (mtp-110) cc_final: 0.7087 (ptp90) REVERT: B 293 THR cc_start: 0.8322 (m) cc_final: 0.7765 (p) REVERT: B 295 ARG cc_start: 0.6402 (mmt180) cc_final: 0.4234 (ttt-90) REVERT: B 417 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6102 (mm-30) REVERT: B 619 MET cc_start: 0.8640 (mtp) cc_final: 0.8368 (mtp) REVERT: B 634 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6651 (pp20) REVERT: B 784 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6785 (pp20) outliers start: 43 outliers final: 24 residues processed: 201 average time/residue: 0.4790 time to fit residues: 104.8759 Evaluate side-chains 195 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [105, 90, 112, 4, 41, 87, 114, 104, 79, 59, 15] chunk 105 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 476 ASN A 568 ASN A 652 HIS B 568 ASN B 652 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136374 restraints weight = 22567.501| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.56 r_work: 0.3353 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10850 Z= 0.121 Angle : 0.600 9.663 14739 Z= 0.307 Chirality : 0.044 0.206 1728 Planarity : 0.004 0.038 1787 Dihedral : 7.036 120.021 1482 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.20 % Allowed : 24.01 % Favored : 72.80 % 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 are not related in a simple way. whole: -0.16 (0.24), residues: 1318 helix: 0.59 (0.19), residues: 836 sheet: -0.71 (0.50), residues: 108 loop : -1.35 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 606 TYR 0.018 0.001 TYR A 288 PHE 0.039 0.001 PHE A 182 TRP 0.012 0.001 TRP A 258 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10850) covalent geometry : angle 0.59973 / 0.31 (14739) hydrogen bonds : bond 0.03523 / 2.29 ( 554) hydrogen bonds : angle 4.38292 / 3.06 ( 1589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.381 Fit side-chains REVERT: A 91 ASP cc_start: 0.6673 (t0) cc_final: 0.6259 (t0) REVERT: A 93 ASP cc_start: 0.7340 (t70) cc_final: 0.6926 (m-30) REVERT: A 119 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 151 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: A 179 ASN cc_start: 0.6838 (m110) cc_final: 0.6232 (p0) REVERT: A 239 PHE cc_start: 0.7589 (m-80) cc_final: 0.7327 (m-80) REVERT: A 241 ARG cc_start: 0.7924 (ptp-110) cc_final: 0.7657 (ptm-80) REVERT: A 293 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7764 (p) REVERT: A 417 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6223 (mm-30) REVERT: A 474 LYS cc_start: 0.4389 (OUTLIER) cc_final: 0.3777 (mttp) REVERT: A 499 MET cc_start: 0.7814 (tpt) cc_final: 0.7390 (mmp) REVERT: A 534 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 575 SER cc_start: 0.8295 (t) cc_final: 0.7981 (p) REVERT: A 581 LEU cc_start: 0.8103 (mm) cc_final: 0.7841 (mt) REVERT: A 619 MET cc_start: 0.8618 (mtp) cc_final: 0.8364 (mtp) REVERT: A 784 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: B 93 ASP cc_start: 0.7266 (t70) cc_final: 0.6784 (m-30) REVERT: B 119 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7461 (mp) REVERT: B 151 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: B 174 LYS cc_start: 0.7370 (tttp) cc_final: 0.7004 (tmtm) REVERT: B 179 ASN cc_start: 0.7188 (m-40) cc_final: 0.6923 (p0) REVERT: B 239 PHE cc_start: 0.7621 (m-80) cc_final: 0.7392 (m-80) REVERT: B 241 ARG cc_start: 0.7885 (ptp-110) cc_final: 0.7612 (ptm-80) REVERT: B 292 ARG cc_start: 0.7396 (mtp-110) cc_final: 0.7122 (ptp90) REVERT: B 295 ARG cc_start: 0.6338 (mmt180) cc_final: 0.4270 (ttt-90) REVERT: B 417 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6213 (mm-30) REVERT: B 499 MET cc_start: 0.7690 (mmm) cc_final: 0.5225 (ptt) REVERT: B 619 MET cc_start: 0.8505 (mtp) cc_final: 0.8213 (mtp) REVERT: B 634 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: B 764 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7577 (mp0) REVERT: B 784 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6839 (pp20) outliers start: 37 outliers final: 22 residues processed: 193 average time/residue: 0.4825 time to fit residues: 101.1182 Evaluate side-chains 192 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 784 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [0, 35, 113, 107, 75, 9, 65, 61, 63, 117, 11] chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 117 optimal weight: 0.0050 chunk 11 optimal weight: 0.0170 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 568 ASN A 652 HIS B 568 ASN B 652 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.165604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142777 restraints weight = 11542.222| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.61 r_work: 0.3433 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10850 Z= 0.109 Angle : 0.580 9.532 14739 Z= 0.297 Chirality : 0.043 0.201 1728 Planarity : 0.004 0.038 1787 Dihedral : 6.901 117.732 1482 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.20 % Allowed : 24.18 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1318 helix: 0.70 (0.19), residues: 836 sheet: -0.54 (0.51), residues: 106 loop : -1.33 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 606 TYR 0.018 0.001 TYR A 288 PHE 0.033 0.001 PHE B 182 TRP 0.012 0.001 TRP A 258 HIS 0.002 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10850) covalent geometry : angle 0.58004 / 0.30 (14739) hydrogen bonds : bond 0.03217 / 2.09 ( 554) hydrogen bonds : angle 4.27675 / 2.98 ( 1589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.84 seconds wall clock time: 69 minutes 23.12 seconds (4163.12 seconds total)