Starting phenix.real_space_refine on Thu Feb 13 13:23:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxi_21438/02_2025/6vxi_21438.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxi_21438/02_2025/6vxi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxi_21438/02_2025/6vxi_21438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxi_21438/02_2025/6vxi_21438.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxi_21438/02_2025/6vxi_21438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxi_21438/02_2025/6vxi_21438.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8898 Number of models: 1 Model: "" Number of chains: 3 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: "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} Restraints were copied for chains: B Time building chain proxies: 8.00, per 1000 atoms: 0.90 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 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: 2.35 Conformation dependent library (CDL) restraints added in 992.6 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: 0.89 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: 2.48 Time building geometry restraints manager: 2.67 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: 516 35.59 - 53.38: 135 53.38 - 71.18: 18 71.18 - 88.97: 10 Dihedral angle restraints: 5461 sinusoidal: 2201 harmonic: 3260 Sorted by residual: 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=" CA ASN B 604 " pdb=" C ASN B 604 " pdb=" N TYR B 605 " pdb=" CA TYR B 605 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASN A 604 " pdb=" C ASN A 604 " pdb=" N TYR A 605 " pdb=" CA TYR A 605 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5458 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: 2.04 - 2.61: 100 2.61 - 3.18: 7536 3.18 - 3.75: 13683 3.75 - 4.33: 18957 4.33 - 4.90: 31303 Nonbonded interactions: 71579 Sorted by model distance: nonbonded pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " model vdw 2.037 3.760 nonbonded pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " model vdw 2.059 3.760 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 ... (remaining 71574 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: 0.660 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.230 Find NCS groups from input model: 0.360 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- 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 9090 Z= 0.546 Angle : 0.998 11.139 12312 Z= 0.502 Chirality : 0.058 0.286 1426 Planarity : 0.005 0.043 1519 Dihedral : 15.952 88.972 3366 Min Nonbonded Distance : 2.037 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.002 TRP B 379 HIS 0.003 0.001 HIS A 375 PHE 0.021 0.003 PHE B 432 TYR 0.019 0.002 TYR A 463 ARG 0.006 0.001 ARG A 184 *********************** 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 : 0.998 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: 0.7715 (mtm110) REVERT: B 353 SER cc_start: 0.5781 (OUTLIER) cc_final: 0.5362 (p) REVERT: B 424 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8617 (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: 0.5992 (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: 0.2236 time to fit residues: 81.6938 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 : 1.022 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123967 restraints weight = 13548.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126726 restraints weight = 8127.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128476 restraints weight = 5815.864| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9090 Z= 0.251 Angle : 0.717 10.319 12312 Z= 0.363 Chirality : 0.043 0.169 1426 Planarity : 0.005 0.030 1519 Dihedral : 6.745 56.288 1355 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.90 % Allowed : 19.09 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.21), residues: 1116 helix: -2.49 (0.17), residues: 570 sheet: -3.83 (0.59), residues: 44 loop : -3.05 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS B 583 PHE 0.023 0.002 PHE B 117 TYR 0.015 0.002 TYR B 605 ARG 0.004 0.000 ARG B 236 *********************** 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 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7426 (mp0) cc_final: 0.7166 (mp0) REVERT: A 250 PHE cc_start: 0.7122 (t80) cc_final: 0.6860 (t80) REVERT: A 612 GLU cc_start: 0.7637 (mp0) cc_final: 0.7356 (mp0) REVERT: B 72 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7533 (mmmt) REVERT: B 138 GLU cc_start: 0.8063 (mp0) cc_final: 0.7626 (mp0) REVERT: B 227 LEU cc_start: 0.8844 (tt) cc_final: 0.8534 (tt) REVERT: B 230 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8245 (mtm110) REVERT: B 454 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8487 (tp) REVERT: B 471 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 523 MET cc_start: 0.9132 (ttt) cc_final: 0.8927 (ttt) REVERT: B 605 TYR cc_start: 0.6590 (m-80) cc_final: 0.6369 (m-10) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.1944 time to fit residues: 59.9030 Evaluate side-chains 198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 299 ASN Chi-restraints excluded: chain A residue 404 VAL 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 165 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 454 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 534 VAL 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 58 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 109 ASN B 289 ASN B 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129651 restraints weight = 13595.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130325 restraints weight = 8008.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131190 restraints weight = 6079.796| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9090 Z= 0.175 Angle : 0.639 9.353 12312 Z= 0.317 Chirality : 0.041 0.170 1426 Planarity : 0.004 0.047 1519 Dihedral : 5.959 49.313 1353 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.53 % Allowed : 19.92 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.23), residues: 1116 helix: -1.48 (0.20), residues: 552 sheet: -3.54 (0.63), residues: 44 loop : -2.81 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.001 0.000 HIS B 155 PHE 0.023 0.002 PHE B 117 TYR 0.015 0.001 TYR A 276 ARG 0.004 0.000 ARG B 236 *********************** 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 234 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8076 (mtp) cc_final: 0.7732 (mtm) REVERT: A 250 PHE cc_start: 0.6993 (t80) cc_final: 0.6730 (t80) REVERT: A 477 ASP cc_start: 0.7548 (t0) cc_final: 0.7237 (t0) REVERT: B 72 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7550 (mmmt) REVERT: B 138 GLU cc_start: 0.7827 (mp0) cc_final: 0.7429 (mp0) REVERT: B 211 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: B 230 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8211 (mtm110) REVERT: B 252 LEU cc_start: 0.8588 (tp) cc_final: 0.8157 (tt) outliers start: 34 outliers final: 21 residues processed: 221 average time/residue: 0.1872 time to fit residues: 59.6222 Evaluate side-chains 206 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 478 LEU 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 135 THR Chi-restraints excluded: chain B residue 165 ILE 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 608 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.162336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130133 restraints weight = 13489.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130760 restraints weight = 8106.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131169 restraints weight = 6332.719| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9090 Z= 0.173 Angle : 0.618 11.114 12312 Z= 0.308 Chirality : 0.041 0.201 1426 Planarity : 0.003 0.041 1519 Dihedral : 5.208 39.228 1352 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.25 % Allowed : 20.23 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.24), residues: 1116 helix: -1.01 (0.22), residues: 560 sheet: -3.35 (0.64), residues: 44 loop : -2.63 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.002 0.000 HIS B 267 PHE 0.027 0.002 PHE B 489 TYR 0.016 0.001 TYR A 276 ARG 0.002 0.000 ARG A 482 *********************** 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 247 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 198 MET cc_start: 0.8078 (mtp) cc_final: 0.7739 (mtp) REVERT: A 252 LEU cc_start: 0.8214 (tp) cc_final: 0.7969 (tt) REVERT: A 477 ASP cc_start: 0.7477 (t0) cc_final: 0.7139 (t0) REVERT: A 565 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8638 (tt) REVERT: B 72 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7529 (mmmt) REVERT: B 138 GLU cc_start: 0.7799 (mp0) cc_final: 0.7551 (mp0) REVERT: B 190 GLU cc_start: 0.6326 (mt-10) cc_final: 0.6117 (mt-10) REVERT: B 252 LEU cc_start: 0.8547 (tp) cc_final: 0.8111 (tt) REVERT: B 477 ASP cc_start: 0.7295 (t0) cc_final: 0.6838 (t0) REVERT: B 523 MET cc_start: 0.8926 (ttt) cc_final: 0.8716 (ttp) REVERT: B 565 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8778 (tt) outliers start: 41 outliers final: 25 residues processed: 228 average time/residue: 0.1827 time to fit residues: 59.4946 Evaluate side-chains 214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 227 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 Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 0.0370 overall best weight: 1.1062 ------------------------------------------------------------------------------- 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 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129491 restraints weight = 13490.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130200 restraints weight = 7787.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130717 restraints weight = 5748.375| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9090 Z= 0.186 Angle : 0.622 12.818 12312 Z= 0.307 Chirality : 0.041 0.178 1426 Planarity : 0.004 0.058 1519 Dihedral : 4.899 38.925 1352 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.56 % Allowed : 20.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.25), residues: 1116 helix: -0.80 (0.21), residues: 574 sheet: -3.39 (0.60), residues: 48 loop : -2.69 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.001 0.000 HIS B 375 PHE 0.023 0.002 PHE B 266 TYR 0.010 0.001 TYR B 459 ARG 0.002 0.000 ARG B 230 *********************** 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: 44 poor density : 196 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 138 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 252 LEU cc_start: 0.8261 (tp) cc_final: 0.8000 (tt) REVERT: A 424 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 477 ASP cc_start: 0.7581 (t0) cc_final: 0.7164 (t0) REVERT: A 565 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 608 CYS cc_start: 0.5135 (p) cc_final: 0.4934 (p) REVERT: B 72 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7536 (mmmt) REVERT: B 190 GLU cc_start: 0.6454 (mt-10) cc_final: 0.6217 (mt-10) REVERT: B 211 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: B 252 LEU cc_start: 0.8646 (tp) cc_final: 0.8252 (tt) REVERT: B 454 LEU cc_start: 0.8970 (tp) cc_final: 0.8662 (tp) REVERT: B 458 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 477 ASP cc_start: 0.7427 (t0) cc_final: 0.6886 (t0) REVERT: B 565 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8808 (tt) outliers start: 44 outliers final: 28 residues processed: 224 average time/residue: 0.1769 time to fit residues: 57.8560 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 : 0.957 ------------------------------------------------------------------------------- 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 371 THR Chi-restraints excluded: chain A residue 389 LEU 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 A residue 592 CYS Chi-restraints excluded: chain B residue 134 LEU 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 227 LEU 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 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 98 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.163651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131030 restraints weight = 13438.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131631 restraints weight = 8330.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131868 restraints weight = 6209.693| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9090 Z= 0.157 Angle : 0.609 12.453 12312 Z= 0.298 Chirality : 0.041 0.181 1426 Planarity : 0.004 0.052 1519 Dihedral : 4.640 38.953 1352 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.88 % Allowed : 19.92 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.25), residues: 1116 helix: -0.63 (0.22), residues: 582 sheet: -2.93 (0.66), residues: 46 loop : -2.52 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 379 HIS 0.002 0.000 HIS B 375 PHE 0.024 0.002 PHE B 266 TYR 0.011 0.001 TYR B 413 ARG 0.003 0.000 ARG B 230 *********************** 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 253 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 138 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: A 252 LEU cc_start: 0.8320 (tp) cc_final: 0.8050 (tt) REVERT: A 477 ASP cc_start: 0.7455 (t0) cc_final: 0.7231 (t0) REVERT: A 565 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8767 (tt) REVERT: B 72 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7414 (mmmt) REVERT: B 107 LEU cc_start: 0.8228 (tp) cc_final: 0.7936 (tp) REVERT: B 211 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: B 405 LEU cc_start: 0.9423 (tp) cc_final: 0.9221 (mt) REVERT: B 452 LYS cc_start: 0.8703 (tttm) cc_final: 0.7839 (ttmt) REVERT: B 454 LEU cc_start: 0.8933 (tp) cc_final: 0.8717 (tp) REVERT: B 458 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: B 477 ASP cc_start: 0.7481 (t0) cc_final: 0.7233 (t0) REVERT: B 540 LEU cc_start: 0.8158 (tp) cc_final: 0.7954 (tp) REVERT: B 565 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8815 (tt) outliers start: 47 outliers final: 29 residues processed: 233 average time/residue: 0.1674 time to fit residues: 57.0051 Evaluate side-chains 218 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LEU 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 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 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 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 0.0070 chunk 12 optimal weight: 0.0570 chunk 6 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3865 r_free = 0.3865 target = 0.166246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134959 restraints weight = 13519.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135109 restraints weight = 8642.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135729 restraints weight = 7122.823| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9090 Z= 0.145 Angle : 0.626 11.746 12312 Z= 0.300 Chirality : 0.041 0.297 1426 Planarity : 0.004 0.052 1519 Dihedral : 4.454 37.891 1352 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 21.89 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.25), residues: 1116 helix: -0.55 (0.22), residues: 588 sheet: -2.53 (0.80), residues: 34 loop : -2.27 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 627 HIS 0.001 0.000 HIS B 375 PHE 0.026 0.002 PHE A 266 TYR 0.019 0.001 TYR A 276 ARG 0.006 0.000 ARG A 236 *********************** 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 234 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (mp) REVERT: A 138 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: A 236 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6919 (mtm110) REVERT: A 252 LEU cc_start: 0.8346 (tp) cc_final: 0.8051 (tt) REVERT: A 509 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7917 (ttt) REVERT: A 565 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8738 (tt) REVERT: B 72 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7402 (mmmt) REVERT: B 107 LEU cc_start: 0.8260 (tp) cc_final: 0.8016 (tp) REVERT: B 211 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 452 LYS cc_start: 0.8714 (tttm) cc_final: 0.7881 (ttmt) REVERT: B 454 LEU cc_start: 0.8907 (tp) cc_final: 0.8700 (tp) REVERT: B 458 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: B 477 ASP cc_start: 0.7488 (t0) cc_final: 0.7226 (t0) REVERT: B 565 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8798 (tt) outliers start: 35 outliers final: 21 residues processed: 220 average time/residue: 0.1853 time to fit residues: 58.7194 Evaluate side-chains 222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 417 LYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE 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 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 458 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 67 optimal weight: 0.0470 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132226 restraints weight = 13689.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132759 restraints weight = 9260.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133196 restraints weight = 7875.676| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9090 Z= 0.180 Angle : 0.652 11.226 12312 Z= 0.314 Chirality : 0.043 0.309 1426 Planarity : 0.004 0.055 1519 Dihedral : 4.501 37.073 1348 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.63 % Allowed : 21.99 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.26), residues: 1116 helix: -0.49 (0.22), residues: 588 sheet: -2.17 (0.70), residues: 46 loop : -2.27 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 627 HIS 0.002 0.000 HIS B 375 PHE 0.025 0.002 PHE A 266 TYR 0.010 0.001 TYR B 413 ARG 0.005 0.000 ARG B 230 *********************** 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 233 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 138 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 152 MET cc_start: 0.7590 (ptp) cc_final: 0.6742 (ptp) REVERT: A 252 LEU cc_start: 0.8383 (tp) cc_final: 0.8092 (tt) REVERT: A 451 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7751 (pt0) REVERT: A 565 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 72 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7428 (mmmt) REVERT: B 107 LEU cc_start: 0.8282 (tp) cc_final: 0.8044 (tp) REVERT: B 154 ASN cc_start: 0.7973 (t0) cc_final: 0.7693 (m110) REVERT: B 211 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: B 452 LYS cc_start: 0.8755 (tttm) cc_final: 0.7928 (ttmt) REVERT: B 454 LEU cc_start: 0.8940 (tp) cc_final: 0.8588 (tt) REVERT: B 458 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: B 477 ASP cc_start: 0.7403 (t0) cc_final: 0.7126 (t0) REVERT: B 565 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8810 (tt) REVERT: B 585 GLU cc_start: 0.8596 (tp30) cc_final: 0.7912 (tp30) outliers start: 35 outliers final: 25 residues processed: 220 average time/residue: 0.1658 time to fit residues: 53.6211 Evaluate side-chains 224 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 423 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE 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 458 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU 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 Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 B 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127990 restraints weight = 13687.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128220 restraints weight = 8598.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128414 restraints weight = 6568.027| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9090 Z= 0.270 Angle : 0.710 10.641 12312 Z= 0.346 Chirality : 0.045 0.280 1426 Planarity : 0.004 0.056 1519 Dihedral : 4.925 38.726 1348 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.94 % Allowed : 22.10 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 1116 helix: -0.47 (0.22), residues: 570 sheet: -2.35 (0.66), residues: 48 loop : -2.30 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.002 0.001 HIS A 243 PHE 0.024 0.002 PHE A 266 TYR 0.014 0.002 TYR B 413 ARG 0.008 0.001 ARG A 236 *********************** 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 232 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 138 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 451 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7811 (pt0) REVERT: A 509 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8363 (ttt) REVERT: A 565 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8595 (tt) REVERT: B 72 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7449 (mmmt) REVERT: B 107 LEU cc_start: 0.8278 (tp) cc_final: 0.7997 (tp) REVERT: B 154 ASN cc_start: 0.8103 (t0) cc_final: 0.7692 (m-40) REVERT: B 211 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: B 454 LEU cc_start: 0.9005 (tp) cc_final: 0.8727 (tp) REVERT: B 458 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: B 477 ASP cc_start: 0.7284 (t0) cc_final: 0.6871 (t0) REVERT: B 565 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8773 (tt) outliers start: 38 outliers final: 26 residues processed: 217 average time/residue: 0.1723 time to fit residues: 55.1033 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 : 0.923 ------------------------------------------------------------------------------- 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 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 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 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 471 LEU Chi-restraints excluded: chain B residue 478 LEU 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 Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127627 restraints weight = 13474.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130412 restraints weight = 7983.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132280 restraints weight = 5673.727| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9090 Z= 0.174 Angle : 0.674 11.086 12312 Z= 0.323 Chirality : 0.043 0.259 1426 Planarity : 0.004 0.059 1519 Dihedral : 4.690 37.151 1348 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.73 % Allowed : 23.13 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.26), residues: 1116 helix: -0.40 (0.22), residues: 566 sheet: -2.42 (0.80), residues: 34 loop : -2.22 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 627 HIS 0.001 0.000 HIS B 375 PHE 0.027 0.002 PHE B 250 TYR 0.014 0.001 TYR B 413 ARG 0.008 0.000 ARG A 236 ********************** 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 228 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 138 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: A 451 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7832 (pt0) REVERT: A 565 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 72 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7413 (mmmt) REVERT: B 107 LEU cc_start: 0.8242 (tp) cc_final: 0.7920 (tp) REVERT: B 154 ASN cc_start: 0.7859 (t0) cc_final: 0.7639 (m110) REVERT: B 211 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 452 LYS cc_start: 0.8763 (tttm) cc_final: 0.7851 (ttmt) REVERT: B 454 LEU cc_start: 0.8936 (tp) cc_final: 0.8568 (tt) REVERT: B 458 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: B 477 ASP cc_start: 0.7360 (t0) cc_final: 0.6955 (t0) REVERT: B 565 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8818 (tt) outliers start: 36 outliers final: 24 residues processed: 215 average time/residue: 0.1687 time to fit residues: 54.8889 Evaluate side-chains 217 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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 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 471 LEU 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 Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 0.0010 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 B 582 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131477 restraints weight = 13427.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131604 restraints weight = 7952.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132326 restraints weight = 6482.467| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9090 Z= 0.187 Angle : 0.681 11.129 12312 Z= 0.328 Chirality : 0.043 0.258 1426 Planarity : 0.004 0.060 1519 Dihedral : 4.710 35.931 1348 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.42 % Allowed : 23.24 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.26), residues: 1116 helix: -0.37 (0.22), residues: 570 sheet: -2.21 (0.81), residues: 34 loop : -2.16 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 627 HIS 0.002 0.000 HIS B 375 PHE 0.028 0.002 PHE A 266 TYR 0.022 0.001 TYR A 276 ARG 0.008 0.000 ARG A 236 =============================================================================== Job complete usr+sys time: 2609.64 seconds wall clock time: 47 minutes 46.33 seconds (2866.33 seconds total)