Starting phenix.real_space_refine on Tue Mar 3 22:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxi_21438/03_2026/6vxi_21438.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxi_21438/03_2026/6vxi_21438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vxi_21438/03_2026/6vxi_21438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxi_21438/03_2026/6vxi_21438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxi_21438/03_2026/6vxi_21438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxi_21438/03_2026/6vxi_21438.map" } resolution = 3.7 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5794 2.51 5 N 1456 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'MIX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8898 At special positions: 0 Unit cell: (104.55, 75.03, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1456 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.06 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: 0.74 Conformation dependent library (CDL) restraints added in 333.8 milliseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 55.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.788A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 4.331A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.103A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.690A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.737A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.653A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.197A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.373A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 278' Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.666A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 4.031A pdb=" N ALA A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.599A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.962A pdb=" N GLY A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.520A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 483 through 498 removed outlier: 5.028A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 527 removed outlier: 3.642A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 543 removed outlier: 3.935A pdb=" N MET A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.723A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.933A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.096A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.701A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.799A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.787A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 4.330A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 4.103A pdb=" N SER B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.688A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.737A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.653A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 220 through 232 removed outlier: 4.196A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.373A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 278' Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.667A pdb=" N PHE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 4.031A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.599A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 413 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 422 through 441 removed outlier: 3.963A pdb=" N GLY B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 446 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 removed outlier: 3.520A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 483 through 498 removed outlier: 5.028A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 527 removed outlier: 3.641A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 543 removed outlier: 3.934A pdb=" N MET B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.724A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.932A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 584 removed outlier: 4.096A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.701A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.799A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 3.861A pdb=" N ASN A 66 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE A 42 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN A 68 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS A 40 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 70 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 38 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.293A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 70 removed outlier: 3.861A pdb=" N ASN B 66 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 42 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN B 68 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS B 40 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 70 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 38 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.293A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1017 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: 1.35 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1384 1.29 - 1.42: 2375 1.42 - 1.55: 5230 1.55 - 1.68: 7 1.68 - 1.81: 94 Bond restraints: 9090 Sorted by residual: bond pdb=" CAY MIX B 701 " pdb=" NAU MIX B 701 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CAZ MIX B 701 " pdb=" NAV MIX B 701 " ideal model delta sigma weight residual 1.343 1.465 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CBA MIX B 701 " pdb=" CBE MIX B 701 " ideal model delta sigma weight residual 1.442 1.554 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CBA MIX B 701 " pdb=" OAA MIX B 701 " ideal model delta sigma weight residual 1.254 1.156 0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" CBB MIX B 701 " pdb=" CBD MIX B 701 " ideal model delta sigma weight residual 1.459 1.552 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 9085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11837 2.23 - 4.46: 403 4.46 - 6.68: 37 6.68 - 8.91: 26 8.91 - 11.14: 9 Bond angle restraints: 12312 Sorted by residual: angle pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP B 217 " pdb=" N SER B 218 " pdb=" CA SER B 218 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N SER A 218 " pdb=" CA SER A 218 " pdb=" C SER A 218 " ideal model delta sigma weight residual 110.80 118.07 -7.27 2.13e+00 2.20e-01 1.16e+01 angle pdb=" N SER B 218 " pdb=" CA SER B 218 " pdb=" C SER B 218 " ideal model delta sigma weight residual 110.80 118.05 -7.25 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C ILE B 108 " pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 ... (remaining 12307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4782 17.79 - 35.59: 517 35.59 - 53.38: 139 53.38 - 71.18: 18 71.18 - 88.97: 11 Dihedral angle restraints: 5467 sinusoidal: 2207 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 18.11 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.23 52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 5464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1043 0.057 - 0.114: 312 0.114 - 0.172: 57 0.172 - 0.229: 8 0.229 - 0.286: 6 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE B 487 " pdb=" CA ILE B 487 " pdb=" CG1 ILE B 487 " pdb=" CG2 ILE B 487 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1423 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 429 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C VAL A 429 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 429 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 430 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 429 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL B 429 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 429 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 430 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 622 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 623 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 623 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 623 " 0.024 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2691 2.81 - 3.33: 8149 3.33 - 3.85: 14395 3.85 - 4.38: 17099 4.38 - 4.90: 29239 Nonbonded interactions: 71573 Sorted by model distance: nonbonded pdb=" OG1 THR B 133 " pdb=" OD1 ASN B 387 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 133 " pdb=" OD1 ASN A 387 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASN B 436 " pdb=" OAD MIX B 701 " model vdw 2.306 3.040 ... (remaining 71568 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 35 through 654) selection = (chain 'B' and resid 35 through 654) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.540 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: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.008 0.149 9093 Z= 0.388 Angle : 1.002 11.139 12318 Z= 0.503 Chirality : 0.058 0.286 1426 Planarity : 0.005 0.043 1519 Dihedral : 15.952 88.972 3366 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.50 % Favored : 90.32 % Rotamer: Outliers : 2.07 % Allowed : 11.83 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.00 (0.17), residues: 1116 helix: -4.44 (0.09), residues: 566 sheet: -4.21 (0.49), residues: 44 loop : -3.26 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 184 TYR 0.019 0.002 TYR A 463 PHE 0.021 0.003 PHE B 432 TRP 0.007 0.002 TRP B 379 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00840 ( 9090) covalent geometry : angle 0.99824 (12312) SS BOND : bond 0.02329 ( 3) SS BOND : angle 3.98788 ( 6) hydrogen bonds : bond 0.31836 ( 355) hydrogen bonds : angle 10.92478 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7721 (ttm) cc_final: 0.7503 (mtp) REVERT: A 230 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7601 (mtm110) REVERT: A 341 PHE cc_start: 0.7454 (m-80) cc_final: 0.7193 (m-80) REVERT: A 509 MET cc_start: 0.8156 (ttt) cc_final: 0.7923 (ttt) REVERT: A 565 LEU cc_start: 0.8828 (tt) cc_final: 0.8616 (tt) REVERT: A 636 MET cc_start: 0.8425 (tpp) cc_final: 0.8222 (mmm) REVERT: B 230 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7717 (mtm110) REVERT: B 353 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5362 (p) REVERT: B 424 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 481 MET cc_start: 0.7821 (mmm) cc_final: 0.7463 (ttt) REVERT: B 523 MET cc_start: 0.9116 (ttt) cc_final: 0.8809 (ttp) REVERT: B 605 TYR cc_start: 0.6641 (m-80) cc_final: 0.5993 (m-10) REVERT: B 636 MET cc_start: 0.8495 (tpp) cc_final: 0.8176 (mmm) outliers start: 20 outliers final: 4 residues processed: 267 average time/residue: 0.0933 time to fit residues: 34.3955 Evaluate side-chains 180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 76 ASN A 109 ASN A 158 ASN A 267 HIS A 299 ASN A 393 GLN A 457 HIS A 583 HIS A 629 ASN B 40 HIS B 109 ASN B 126 GLN B 158 ASN B 267 HIS B 299 ASN B 393 GLN B 457 HIS B 583 HIS B 629 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127849 restraints weight = 13538.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128898 restraints weight = 8858.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130002 restraints weight = 6609.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130688 restraints weight = 5443.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130890 restraints weight = 5167.699| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9093 Z= 0.143 Angle : 0.702 10.271 12318 Z= 0.353 Chirality : 0.042 0.187 1426 Planarity : 0.004 0.030 1519 Dihedral : 6.724 57.927 1355 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.49 % Allowed : 18.46 % Favored : 79.05 % 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: -4.23 (0.21), residues: 1116 helix: -2.47 (0.17), residues: 570 sheet: -3.66 (0.62), residues: 44 loop : -3.07 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.014 0.001 TYR B 247 PHE 0.024 0.002 PHE B 117 TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9090) covalent geometry : angle 0.70204 (12312) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.94001 ( 6) hydrogen bonds : bond 0.04531 ( 355) hydrogen bonds : angle 5.43432 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7392 (mp0) cc_final: 0.7122 (mp0) REVERT: A 250 PHE cc_start: 0.7152 (t80) cc_final: 0.6869 (t80) REVERT: A 612 GLU cc_start: 0.7589 (mp0) cc_final: 0.7335 (mp0) REVERT: B 72 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7516 (mmmt) REVERT: B 138 GLU cc_start: 0.8038 (mp0) cc_final: 0.7623 (mp0) REVERT: B 227 LEU cc_start: 0.8865 (tt) cc_final: 0.8576 (tt) REVERT: B 230 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8249 (mtm110) REVERT: B 471 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8756 (mp) REVERT: B 523 MET cc_start: 0.9108 (ttt) cc_final: 0.8847 (ttp) outliers start: 24 outliers final: 14 residues processed: 218 average time/residue: 0.0809 time to fit residues: 25.5479 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.0020 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 289 ASN B 76 ASN B 109 ASN B 126 GLN B 289 ASN B 391 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131829 restraints weight = 13521.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132358 restraints weight = 8045.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132786 restraints weight = 6196.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.133072 restraints weight = 5385.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133226 restraints weight = 5073.382| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9093 Z= 0.115 Angle : 0.623 9.450 12318 Z= 0.308 Chirality : 0.041 0.166 1426 Planarity : 0.004 0.047 1519 Dihedral : 5.823 51.881 1353 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.80 % Allowed : 20.12 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.23), residues: 1116 helix: -1.53 (0.20), residues: 564 sheet: -3.49 (0.64), residues: 44 loop : -2.86 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.016 0.001 TYR A 276 PHE 0.026 0.002 PHE B 489 TRP 0.009 0.001 TRP B 379 HIS 0.001 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9090) covalent geometry : angle 0.62321 (12312) SS BOND : bond 0.00219 ( 3) SS BOND : angle 0.66009 ( 6) hydrogen bonds : bond 0.03900 ( 355) hydrogen bonds : angle 4.83534 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.305 Fit side-chains REVERT: A 138 GLU cc_start: 0.7977 (mp0) cc_final: 0.7668 (mp0) REVERT: A 252 LEU cc_start: 0.8203 (tp) cc_final: 0.7931 (tt) REVERT: A 477 ASP cc_start: 0.7539 (t0) cc_final: 0.7257 (t0) REVERT: A 514 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7136 (ptp) REVERT: B 72 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7524 (mmmt) REVERT: B 211 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: B 230 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8235 (mtm110) REVERT: B 252 LEU cc_start: 0.8541 (tp) cc_final: 0.8123 (tt) REVERT: B 452 LYS cc_start: 0.8694 (tttp) cc_final: 0.8460 (tttm) REVERT: B 499 LEU cc_start: 0.8128 (mt) cc_final: 0.7890 (mt) REVERT: B 585 GLU cc_start: 0.8677 (tp30) cc_final: 0.8329 (tp30) outliers start: 27 outliers final: 16 residues processed: 221 average time/residue: 0.0731 time to fit residues: 23.7565 Evaluate side-chains 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 116 ASN A 391 ASN B 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131424 restraints weight = 13607.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131833 restraints weight = 9223.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132993 restraints weight = 6893.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133126 restraints weight = 5416.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133326 restraints weight = 4972.530| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9093 Z= 0.120 Angle : 0.618 10.724 12318 Z= 0.306 Chirality : 0.041 0.171 1426 Planarity : 0.004 0.057 1519 Dihedral : 5.151 42.029 1352 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.15 % Allowed : 20.75 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.24), residues: 1116 helix: -1.05 (0.21), residues: 582 sheet: -3.41 (0.63), residues: 46 loop : -2.68 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.035 0.001 TYR A 518 PHE 0.022 0.002 PHE B 266 TRP 0.011 0.001 TRP B 379 HIS 0.001 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9090) covalent geometry : angle 0.61771 (12312) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.60853 ( 6) hydrogen bonds : bond 0.03563 ( 355) hydrogen bonds : angle 4.56377 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: A 252 LEU cc_start: 0.8287 (tp) cc_final: 0.7980 (tt) REVERT: A 424 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 477 ASP cc_start: 0.7435 (t0) cc_final: 0.7070 (t0) REVERT: A 565 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8629 (tt) REVERT: B 72 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7440 (mmmt) REVERT: B 211 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 230 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8228 (mtm110) REVERT: B 252 LEU cc_start: 0.8669 (tp) cc_final: 0.8294 (tt) REVERT: B 452 LYS cc_start: 0.8701 (tttp) cc_final: 0.7909 (ttmt) REVERT: B 470 PHE cc_start: 0.8947 (t80) cc_final: 0.8700 (t80) REVERT: B 477 ASP cc_start: 0.7295 (t0) cc_final: 0.6869 (t0) REVERT: B 565 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8801 (tt) REVERT: B 585 GLU cc_start: 0.8736 (tp30) cc_final: 0.8428 (tp30) outliers start: 40 outliers final: 25 residues processed: 233 average time/residue: 0.0744 time to fit residues: 25.5490 Evaluate side-chains 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 0.0670 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 116 ASN B 76 ASN B 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131197 restraints weight = 13581.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130725 restraints weight = 10641.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131719 restraints weight = 8156.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132064 restraints weight = 6687.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132282 restraints weight = 5811.332| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9093 Z= 0.142 Angle : 0.649 13.014 12318 Z= 0.319 Chirality : 0.042 0.194 1426 Planarity : 0.004 0.051 1519 Dihedral : 4.975 39.611 1352 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.88 % Allowed : 21.06 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.68 (0.25), residues: 1116 helix: -0.91 (0.21), residues: 592 sheet: -3.36 (0.61), residues: 48 loop : -2.72 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 426 TYR 0.029 0.001 TYR A 518 PHE 0.023 0.002 PHE B 266 TRP 0.010 0.001 TRP B 379 HIS 0.001 0.000 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9090) covalent geometry : angle 0.64793 (12312) SS BOND : bond 0.00212 ( 3) SS BOND : angle 1.80416 ( 6) hydrogen bonds : bond 0.03583 ( 355) hydrogen bonds : angle 4.53863 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7882 (mp) REVERT: A 138 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 199 GLU cc_start: 0.7433 (mp0) cc_final: 0.7201 (mp0) REVERT: A 252 LEU cc_start: 0.8224 (tp) cc_final: 0.7943 (tt) REVERT: A 477 ASP cc_start: 0.7577 (t0) cc_final: 0.7249 (t0) REVERT: A 565 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 585 GLU cc_start: 0.8265 (tp30) cc_final: 0.8061 (tp30) REVERT: A 608 CYS cc_start: 0.4967 (p) cc_final: 0.4731 (p) REVERT: B 72 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7457 (mmmt) REVERT: B 211 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 252 LEU cc_start: 0.8677 (tp) cc_final: 0.8233 (tt) REVERT: B 458 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: B 565 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8792 (tt) outliers start: 47 outliers final: 29 residues processed: 224 average time/residue: 0.0729 time to fit residues: 24.2118 Evaluate side-chains 220 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 109 ASN A 387 ASN B 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.158761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125544 restraints weight = 13654.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126081 restraints weight = 9483.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126659 restraints weight = 7831.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127111 restraints weight = 5885.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127269 restraints weight = 5461.313| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9093 Z= 0.206 Angle : 0.698 9.643 12318 Z= 0.346 Chirality : 0.044 0.181 1426 Planarity : 0.004 0.053 1519 Dihedral : 5.312 38.739 1352 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.98 % Allowed : 21.58 % Favored : 73.44 % 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: -2.54 (0.25), residues: 1116 helix: -0.77 (0.21), residues: 574 sheet: -3.42 (0.56), residues: 48 loop : -2.62 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.020 0.002 TYR A 518 PHE 0.021 0.002 PHE A 266 TRP 0.010 0.002 TRP B 379 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 9090) covalent geometry : angle 0.69722 (12312) SS BOND : bond 0.00493 ( 3) SS BOND : angle 1.40012 ( 6) hydrogen bonds : bond 0.03822 ( 355) hydrogen bonds : angle 4.65755 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.287 Fit side-chains REVERT: A 134 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 138 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 154 ASN cc_start: 0.8038 (t0) cc_final: 0.7834 (t0) REVERT: A 477 ASP cc_start: 0.7705 (t0) cc_final: 0.7204 (t0) REVERT: A 565 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8583 (tt) REVERT: B 72 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7467 (mmmt) REVERT: B 211 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 565 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8747 (tt) outliers start: 48 outliers final: 32 residues processed: 219 average time/residue: 0.0651 time to fit residues: 21.5813 Evaluate side-chains 210 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131137 restraints weight = 13661.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131266 restraints weight = 9045.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132074 restraints weight = 6939.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132369 restraints weight = 5623.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132621 restraints weight = 4985.458| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9093 Z= 0.125 Angle : 0.666 14.004 12318 Z= 0.324 Chirality : 0.042 0.188 1426 Planarity : 0.004 0.055 1519 Dihedral : 4.911 37.840 1352 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.67 % Allowed : 21.78 % Favored : 73.55 % 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: -2.29 (0.25), residues: 1116 helix: -0.59 (0.22), residues: 582 sheet: -3.06 (0.60), residues: 48 loop : -2.51 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 236 TYR 0.019 0.001 TYR A 518 PHE 0.026 0.002 PHE B 266 TRP 0.007 0.001 TRP B 627 HIS 0.001 0.000 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9090) covalent geometry : angle 0.66429 (12312) SS BOND : bond 0.00877 ( 3) SS BOND : angle 2.09147 ( 6) hydrogen bonds : bond 0.03506 ( 355) hydrogen bonds : angle 4.61490 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 138 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: A 154 ASN cc_start: 0.7944 (t0) cc_final: 0.7706 (t0) REVERT: A 565 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8692 (tt) REVERT: B 72 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7440 (mmmt) REVERT: B 211 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: B 231 MET cc_start: 0.8341 (mpp) cc_final: 0.8138 (mpp) REVERT: B 452 LYS cc_start: 0.8747 (tttm) cc_final: 0.7914 (ttmt) REVERT: B 458 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6147 (mt-10) REVERT: B 565 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8758 (tt) outliers start: 45 outliers final: 29 residues processed: 225 average time/residue: 0.0722 time to fit residues: 24.2084 Evaluate side-chains 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.128442 restraints weight = 13524.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129444 restraints weight = 10007.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130538 restraints weight = 7021.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130487 restraints weight = 5347.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130642 restraints weight = 5130.431| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9093 Z= 0.179 Angle : 0.716 11.587 12318 Z= 0.351 Chirality : 0.044 0.188 1426 Planarity : 0.004 0.056 1519 Dihedral : 5.118 37.701 1352 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.77 % Allowed : 21.37 % Favored : 73.86 % 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: -2.20 (0.25), residues: 1116 helix: -0.55 (0.22), residues: 568 sheet: -2.83 (0.60), residues: 48 loop : -2.39 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 236 TYR 0.019 0.002 TYR A 276 PHE 0.024 0.002 PHE A 266 TRP 0.007 0.001 TRP B 627 HIS 0.002 0.000 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9090) covalent geometry : angle 0.71525 (12312) SS BOND : bond 0.00210 ( 3) SS BOND : angle 1.73839 ( 6) hydrogen bonds : bond 0.03713 ( 355) hydrogen bonds : angle 4.67227 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 138 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 565 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8546 (tt) REVERT: B 72 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7496 (mmmt) REVERT: B 107 LEU cc_start: 0.8264 (tp) cc_final: 0.8019 (tp) REVERT: B 211 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 452 LYS cc_start: 0.8792 (tttm) cc_final: 0.7949 (ttmt) REVERT: B 477 ASP cc_start: 0.7156 (t70) cc_final: 0.6804 (t0) REVERT: B 565 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 585 GLU cc_start: 0.8468 (tp30) cc_final: 0.8266 (tp30) outliers start: 46 outliers final: 34 residues processed: 221 average time/residue: 0.0704 time to fit residues: 23.4110 Evaluate side-chains 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130500 restraints weight = 13545.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131836 restraints weight = 9413.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132856 restraints weight = 6576.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132775 restraints weight = 5086.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132941 restraints weight = 4749.180| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9093 Z= 0.128 Angle : 0.692 11.540 12318 Z= 0.334 Chirality : 0.043 0.193 1426 Planarity : 0.004 0.060 1519 Dihedral : 4.888 37.723 1352 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.36 % Allowed : 21.99 % Favored : 73.65 % 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: -2.09 (0.26), residues: 1116 helix: -0.41 (0.22), residues: 562 sheet: -2.51 (0.64), residues: 48 loop : -2.42 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 236 TYR 0.023 0.001 TYR A 276 PHE 0.027 0.002 PHE B 266 TRP 0.007 0.001 TRP B 627 HIS 0.014 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9090) covalent geometry : angle 0.69195 (12312) SS BOND : bond 0.00234 ( 3) SS BOND : angle 1.32591 ( 6) hydrogen bonds : bond 0.03490 ( 355) hydrogen bonds : angle 4.63800 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 138 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 494 TYR cc_start: 0.8623 (t80) cc_final: 0.8350 (t80) REVERT: A 565 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 72 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7451 (mmmt) REVERT: B 107 LEU cc_start: 0.8254 (tp) cc_final: 0.8001 (tp) REVERT: B 211 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 446 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6124 (tm-30) REVERT: B 452 LYS cc_start: 0.8748 (tttm) cc_final: 0.7887 (ttmt) REVERT: B 477 ASP cc_start: 0.7346 (t70) cc_final: 0.6944 (t0) REVERT: B 565 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8773 (tt) outliers start: 42 outliers final: 29 residues processed: 224 average time/residue: 0.0723 time to fit residues: 24.4063 Evaluate side-chains 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 90 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128228 restraints weight = 13417.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130944 restraints weight = 8025.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132805 restraints weight = 5729.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133819 restraints weight = 4617.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134664 restraints weight = 4065.126| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9093 Z= 0.121 Angle : 0.686 12.176 12318 Z= 0.331 Chirality : 0.043 0.196 1426 Planarity : 0.004 0.063 1519 Dihedral : 4.741 36.537 1352 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.84 % Allowed : 21.99 % Favored : 74.17 % 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: -2.02 (0.26), residues: 1116 helix: -0.42 (0.22), residues: 568 sheet: -2.04 (0.71), residues: 46 loop : -2.37 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 236 TYR 0.020 0.001 TYR A 276 PHE 0.026 0.002 PHE B 266 TRP 0.006 0.001 TRP B 627 HIS 0.010 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9090) covalent geometry : angle 0.68506 (12312) SS BOND : bond 0.00239 ( 3) SS BOND : angle 1.47398 ( 6) hydrogen bonds : bond 0.03433 ( 355) hydrogen bonds : angle 4.63895 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 138 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 565 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8729 (tt) REVERT: B 72 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7407 (mmmt) REVERT: B 107 LEU cc_start: 0.8257 (tp) cc_final: 0.8024 (tp) REVERT: B 211 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 446 GLU cc_start: 0.6195 (tm-30) cc_final: 0.5950 (tm-30) REVERT: B 451 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7815 (pt0) REVERT: B 452 LYS cc_start: 0.8717 (tttm) cc_final: 0.7887 (ttmt) REVERT: B 477 ASP cc_start: 0.7321 (t70) cc_final: 0.6928 (t0) REVERT: B 514 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7251 (ptp) REVERT: B 565 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8791 (tt) outliers start: 37 outliers final: 27 residues processed: 224 average time/residue: 0.0694 time to fit residues: 23.3583 Evaluate side-chains 219 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 7.9990 chunk 50 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 79 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 overall best weight: 2.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 126 GLN B 584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126169 restraints weight = 13347.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126404 restraints weight = 8470.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126878 restraints weight = 6068.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126969 restraints weight = 5540.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128419 restraints weight = 5296.725| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9093 Z= 0.203 Angle : 0.753 11.816 12318 Z= 0.368 Chirality : 0.046 0.193 1426 Planarity : 0.004 0.063 1519 Dihedral : 5.151 37.633 1352 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.73 % Allowed : 22.61 % Favored : 73.65 % 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: -2.09 (0.26), residues: 1116 helix: -0.46 (0.22), residues: 566 sheet: -2.25 (0.67), residues: 48 loop : -2.39 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 236 TYR 0.021 0.002 TYR A 276 PHE 0.024 0.002 PHE A 266 TRP 0.007 0.001 TRP B 627 HIS 0.010 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9090) covalent geometry : angle 0.75138 (12312) SS BOND : bond 0.00290 ( 3) SS BOND : angle 2.02529 ( 6) hydrogen bonds : bond 0.03739 ( 355) hydrogen bonds : angle 4.69828 ( 1017) =============================================================================== Job complete usr+sys time: 1364.30 seconds wall clock time: 24 minutes 18.13 seconds (1458.13 seconds total)