Starting phenix.real_space_refine on Sat Dec 28 19:45:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxi_21438/12_2024/6vxi_21438.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxi_21438/12_2024/6vxi_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_21438/12_2024/6vxi_21438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxi_21438/12_2024/6vxi_21438.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxi_21438/12_2024/6vxi_21438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxi_21438/12_2024/6vxi_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-5532/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: 8.17, per 1000 atoms: 0.92 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.56 Time building geometry restraints manager: 2.79 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: 1.350 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: 0.020 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.760 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.670 ------------------------------------------------------------------------------- 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 : 1.020 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: 0.2270 time to fit residues: 81.6466 Evaluate side-chains 180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7375 (mp0) cc_final: 0.7099 (mp0) REVERT: A 250 PHE cc_start: 0.7012 (t80) cc_final: 0.6797 (t80) REVERT: A 612 GLU cc_start: 0.7525 (mp0) cc_final: 0.7279 (mp0) REVERT: B 72 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7541 (mmmt) REVERT: B 138 GLU cc_start: 0.7967 (mp0) cc_final: 0.7582 (mp0) REVERT: B 227 LEU cc_start: 0.8792 (tt) cc_final: 0.8472 (tt) REVERT: B 230 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8197 (mtm110) REVERT: B 454 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8480 (tp) REVERT: B 471 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 605 TYR cc_start: 0.6574 (m-80) cc_final: 0.6364 (m-10) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.1919 time to fit residues: 59.0317 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 : 1.038 ------------------------------------------------------------------------------- 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 56 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 B 109 ASN B 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9090 Z= 0.303 Angle : 0.700 9.255 12312 Z= 0.352 Chirality : 0.043 0.166 1426 Planarity : 0.004 0.047 1519 Dihedral : 6.095 44.256 1353 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.56 % Allowed : 20.23 % 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: -3.27 (0.23), residues: 1116 helix: -1.50 (0.21), residues: 540 sheet: -4.00 (0.53), residues: 48 loop : -2.71 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.002 0.001 HIS B 155 PHE 0.024 0.002 PHE B 117 TYR 0.015 0.002 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 239 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7854 (mp0) cc_final: 0.7645 (mp0) REVERT: A 198 MET cc_start: 0.8151 (mtp) cc_final: 0.7905 (mtp) REVERT: A 477 ASP cc_start: 0.7405 (t0) cc_final: 0.7052 (t0) REVERT: A 565 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8581 (tt) REVERT: A 636 MET cc_start: 0.8364 (mtp) cc_final: 0.8015 (mtp) REVERT: B 72 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7578 (mmmt) REVERT: B 211 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: B 230 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8145 (mtm110) REVERT: B 523 MET cc_start: 0.8950 (ttt) cc_final: 0.8684 (ttp) outliers start: 44 outliers final: 28 residues processed: 221 average time/residue: 0.1904 time to fit residues: 60.0386 Evaluate side-chains 208 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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 108 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 401 VAL 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 76 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 289 ASN A 387 ASN B 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2890 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= 0.161 Angle : 0.613 11.481 12312 Z= 0.305 Chirality : 0.041 0.201 1426 Planarity : 0.004 0.049 1519 Dihedral : 5.138 39.231 1352 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.63 % Allowed : 21.27 % 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: -2.85 (0.24), residues: 1116 helix: -0.99 (0.22), residues: 552 sheet: -3.58 (0.59), residues: 44 loop : -2.76 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.000 HIS B 267 PHE 0.026 0.002 PHE A 578 TYR 0.017 0.001 TYR A 276 ARG 0.001 0.000 ARG B 246 *********************** 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: 35 poor density : 212 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7862 (t-170) REVERT: A 117 PHE cc_start: 0.8400 (t80) cc_final: 0.8178 (t80) REVERT: A 138 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: A 198 MET cc_start: 0.8017 (mtp) cc_final: 0.7737 (mtp) REVERT: A 477 ASP cc_start: 0.7462 (t0) cc_final: 0.7096 (t0) REVERT: A 585 GLU cc_start: 0.8232 (tp30) cc_final: 0.7952 (tp30) REVERT: B 72 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7505 (mmmt) REVERT: B 190 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6243 (mt-10) REVERT: B 227 LEU cc_start: 0.8482 (tt) cc_final: 0.8169 (tt) REVERT: B 252 LEU cc_start: 0.8518 (tp) cc_final: 0.8117 (tt) REVERT: B 452 LYS cc_start: 0.8737 (tttp) cc_final: 0.8293 (ttmm) REVERT: B 565 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8741 (tt) outliers start: 35 outliers final: 19 residues processed: 231 average time/residue: 0.2090 time to fit residues: 68.5441 Evaluate side-chains 210 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE 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 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 61 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 299 ASN A 391 ASN B 41 ASN B 387 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9090 Z= 0.340 Angle : 0.717 11.641 12312 Z= 0.357 Chirality : 0.045 0.184 1426 Planarity : 0.004 0.051 1519 Dihedral : 5.581 38.921 1352 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.81 % Allowed : 20.02 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.67 (0.25), residues: 1116 helix: -0.84 (0.22), residues: 562 sheet: -3.81 (0.54), residues: 48 loop : -2.65 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 379 HIS 0.002 0.001 HIS B 155 PHE 0.021 0.002 PHE B 266 TYR 0.029 0.002 TYR A 518 ARG 0.003 0.001 ARG B 426 *********************** 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 249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7840 (t-170) REVERT: A 154 ASN cc_start: 0.7986 (t0) cc_final: 0.7758 (t0) REVERT: A 477 ASP cc_start: 0.7681 (t0) cc_final: 0.7183 (t0) REVERT: A 518 TYR cc_start: 0.8488 (m-80) cc_final: 0.8237 (m-80) REVERT: A 565 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8568 (tt) REVERT: B 72 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7568 (mmmt) REVERT: B 190 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6416 (mt-10) REVERT: B 211 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 225 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7780 (tp) REVERT: B 452 LYS cc_start: 0.8867 (tttp) cc_final: 0.8056 (ttmt) REVERT: B 458 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: B 471 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8880 (mp) REVERT: B 565 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8597 (tt) outliers start: 56 outliers final: 37 residues processed: 227 average time/residue: 0.1772 time to fit residues: 58.4040 Evaluate side-chains 222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 GLU 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 446 GLU Chi-restraints excluded: chain A residue 471 LEU 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 37 LEU 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 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 265 MET 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 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 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.0050 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 overall best weight: 0.5252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9090 Z= 0.163 Angle : 0.646 12.518 12312 Z= 0.316 Chirality : 0.042 0.183 1426 Planarity : 0.003 0.052 1519 Dihedral : 4.917 38.496 1352 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.67 % Allowed : 21.16 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.44 (0.25), residues: 1116 helix: -0.64 (0.22), residues: 562 sheet: -3.49 (0.56), residues: 48 loop : -2.58 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 379 HIS 0.001 0.000 HIS A 583 PHE 0.020 0.002 PHE B 266 TYR 0.016 0.001 TYR A 518 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 254 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7854 (t-170) REVERT: A 134 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 138 GLU cc_start: 0.7906 (mp0) cc_final: 0.7705 (mp0) REVERT: A 154 ASN cc_start: 0.7939 (t0) cc_final: 0.7716 (t0) REVERT: A 565 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 72 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7510 (mmmt) REVERT: B 211 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 452 LYS cc_start: 0.8761 (tttp) cc_final: 0.8267 (ttmm) REVERT: B 458 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: B 540 LEU cc_start: 0.8235 (tp) cc_final: 0.8011 (tp) REVERT: B 565 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8750 (tt) outliers start: 45 outliers final: 29 residues processed: 233 average time/residue: 0.1767 time to fit residues: 60.1045 Evaluate side-chains 226 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR 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 478 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0020 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9090 Z= 0.221 Angle : 0.688 11.119 12312 Z= 0.338 Chirality : 0.043 0.179 1426 Planarity : 0.004 0.057 1519 Dihedral : 4.938 38.049 1352 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.88 % Allowed : 20.54 % Favored : 74.59 % 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: -0.51 (0.22), residues: 560 sheet: -3.33 (0.55), residues: 48 loop : -2.54 (0.28), residues: 508 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 0.023 0.002 PHE B 266 TYR 0.029 0.001 TYR A 518 ARG 0.002 0.000 ARG B 230 *********************** 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 240 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7850 (t-170) REVERT: A 134 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7948 (mp) REVERT: A 154 ASN cc_start: 0.7935 (t0) cc_final: 0.7721 (t0) REVERT: A 252 LEU cc_start: 0.8199 (tp) cc_final: 0.7851 (tt) REVERT: A 565 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 72 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7457 (mmmt) REVERT: B 211 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 454 LEU cc_start: 0.8887 (tp) cc_final: 0.8300 (tt) REVERT: B 458 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: B 565 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8728 (tt) outliers start: 47 outliers final: 33 residues processed: 219 average time/residue: 0.1804 time to fit residues: 58.0246 Evaluate side-chains 222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 134 LEU 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 256 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 GLU 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 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 226 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9090 Z= 0.285 Angle : 0.712 10.264 12312 Z= 0.352 Chirality : 0.044 0.189 1426 Planarity : 0.004 0.059 1519 Dihedral : 5.210 38.204 1352 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.29 % Allowed : 21.06 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.32 (0.25), residues: 1116 helix: -0.56 (0.22), residues: 560 sheet: -3.13 (0.56), residues: 48 loop : -2.53 (0.28), residues: 508 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 0.017 0.002 PHE B 385 TYR 0.021 0.002 TYR A 518 ARG 0.003 0.000 ARG B 426 *********************** 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 242 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (t-170) REVERT: A 134 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (mp) REVERT: A 565 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8546 (tt) REVERT: B 72 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7469 (mmmt) REVERT: B 211 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: B 454 LEU cc_start: 0.8907 (tp) cc_final: 0.8630 (tt) REVERT: B 458 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: B 565 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8607 (tt) REVERT: B 585 GLU cc_start: 0.8478 (tp30) cc_final: 0.8259 (tp30) outliers start: 51 outliers final: 35 residues processed: 220 average time/residue: 0.1730 time to fit residues: 55.8333 Evaluate side-chains 225 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 37 LEU 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 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 106 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9090 Z= 0.175 Angle : 0.670 11.116 12312 Z= 0.324 Chirality : 0.042 0.190 1426 Planarity : 0.004 0.056 1519 Dihedral : 4.881 37.239 1352 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.15 % Allowed : 21.99 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.15 (0.25), residues: 1116 helix: -0.41 (0.22), residues: 560 sheet: -2.61 (0.63), residues: 44 loop : -2.52 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 627 HIS 0.012 0.001 HIS B 40 PHE 0.024 0.002 PHE A 266 TYR 0.021 0.001 TYR A 518 ARG 0.002 0.000 ARG B 96 *********************** 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 236 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7869 (t-170) REVERT: A 134 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 252 LEU cc_start: 0.8146 (tp) cc_final: 0.7758 (tt) REVERT: A 565 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 608 CYS cc_start: 0.5393 (p) cc_final: 0.5130 (p) REVERT: B 72 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7420 (mmmt) REVERT: B 211 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: B 452 LYS cc_start: 0.8792 (tttm) cc_final: 0.7949 (ttmt) REVERT: B 454 LEU cc_start: 0.8852 (tp) cc_final: 0.8257 (tt) REVERT: B 458 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: B 565 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8689 (tt) outliers start: 40 outliers final: 31 residues processed: 216 average time/residue: 0.1758 time to fit residues: 56.1416 Evaluate side-chains 232 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR 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 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 256 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 493 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9090 Z= 0.306 Angle : 0.737 12.942 12312 Z= 0.361 Chirality : 0.046 0.190 1426 Planarity : 0.004 0.056 1519 Dihedral : 5.238 36.771 1352 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.36 % Allowed : 21.68 % 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: -2.22 (0.25), residues: 1116 helix: -0.51 (0.22), residues: 566 sheet: -2.85 (0.59), residues: 48 loop : -2.48 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 627 HIS 0.012 0.001 HIS B 40 PHE 0.016 0.002 PHE B 385 TYR 0.019 0.002 TYR A 276 ARG 0.004 0.000 ARG B 426 ********************** 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: 42 poor density : 186 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7874 (t-170) REVERT: A 154 ASN cc_start: 0.7877 (t0) cc_final: 0.7669 (t0) REVERT: A 565 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 608 CYS cc_start: 0.5238 (p) cc_final: 0.5009 (p) REVERT: B 72 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7446 (mmmt) REVERT: B 211 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: B 446 GLU cc_start: 0.6309 (tm-30) cc_final: 0.6077 (tm-30) REVERT: B 458 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: B 565 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8574 (tt) outliers start: 42 outliers final: 34 residues processed: 212 average time/residue: 0.1673 time to fit residues: 52.5579 Evaluate side-chains 223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 256 LEU 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 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 37 LEU 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 225 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 256 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 493 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 37 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126623 restraints weight = 13372.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129300 restraints weight = 8049.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130953 restraints weight = 5781.993| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9090 Z= 0.172 Angle : 0.682 12.350 12312 Z= 0.328 Chirality : 0.043 0.193 1426 Planarity : 0.004 0.057 1519 Dihedral : 4.888 36.138 1352 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.36 % Allowed : 21.78 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.07 (0.25), residues: 1116 helix: -0.35 (0.22), residues: 560 sheet: -2.29 (0.68), residues: 44 loop : -2.50 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 627 HIS 0.009 0.001 HIS B 40 PHE 0.027 0.002 PHE B 250 TYR 0.021 0.001 TYR A 518 ARG 0.002 0.000 ARG B 96 =============================================================================== Job complete usr+sys time: 1929.61 seconds wall clock time: 36 minutes 20.97 seconds (2180.97 seconds total)