Starting phenix.real_space_refine on Fri Sep 11 10:32:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxi_21438/09_2026/6vxi_21438.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5794 2.51 5 N 1456 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'MIX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8898 At special positions: 0 Unit cell: (104.55, 75.03, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1456 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 326.7 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: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.788A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 4.331A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.103A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.690A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.737A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.653A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.197A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.373A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 278' Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.666A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 4.031A pdb=" N ALA A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.599A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.962A pdb=" N GLY A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.520A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 483 through 498 removed outlier: 5.028A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 527 removed outlier: 3.642A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 543 removed outlier: 3.935A pdb=" N MET A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.723A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.933A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.096A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.701A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.799A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.787A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 4.330A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 4.103A pdb=" N SER B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.688A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.737A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.653A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 220 through 232 removed outlier: 4.196A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.373A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 278' Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.667A pdb=" N PHE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 4.031A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.599A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 413 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 422 through 441 removed outlier: 3.963A pdb=" N GLY B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 446 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 removed outlier: 3.520A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 483 through 498 removed outlier: 5.028A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 527 removed outlier: 3.641A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 543 removed outlier: 3.934A pdb=" N MET B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.724A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.932A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 584 removed outlier: 4.096A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.701A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.799A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 3.861A pdb=" N ASN A 66 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE A 42 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN A 68 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS A 40 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 70 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 38 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.293A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 70 removed outlier: 3.861A pdb=" N ASN B 66 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 42 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN B 68 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS B 40 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 70 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 38 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.293A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.03 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: 4686 17.79 - 35.59: 505 35.59 - 53.38: 135 53.38 - 71.18: 18 71.18 - 88.97: 11 Dihedral angle restraints: 5355 sinusoidal: 2095 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 18.11 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.23 52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 5352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1043 0.057 - 0.114: 312 0.114 - 0.172: 57 0.172 - 0.229: 8 0.229 - 0.286: 6 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE B 487 " pdb=" CA ILE B 487 " pdb=" CG1 ILE B 487 " pdb=" CG2 ILE B 487 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1423 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 429 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C VAL A 429 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 429 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 430 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 429 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL B 429 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 429 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 430 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 622 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 623 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 623 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 623 " 0.024 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2691 2.81 - 3.33: 8149 3.33 - 3.85: 14395 3.85 - 4.38: 17099 4.38 - 4.90: 29239 Nonbonded interactions: 71573 Sorted by model distance: nonbonded pdb=" OG1 THR B 133 " pdb=" OD1 ASN B 387 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 133 " pdb=" OD1 ASN A 387 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASN B 436 " pdb=" OAD MIX B 701 " model vdw 2.306 3.040 ... (remaining 71568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 654) selection = (chain 'B' and resid 35 through 654) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.149 9093 Z= 0.388 Angle : 1.002 11.139 12318 Z= 0.503 Chirality : 0.058 0.286 1426 Planarity : 0.005 0.043 1519 Dihedral : 15.999 88.972 3254 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.50 % Favored : 90.32 % Rotamer: Outliers : 2.07 % Allowed : 11.83 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.00 (0.17), residues: 1116 helix: -4.44 (0.09), residues: 566 sheet: -4.21 (0.49), residues: 44 loop : -3.26 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 184 TYR 0.019 0.002 TYR A 463 PHE 0.021 0.003 PHE B 432 TRP 0.007 0.002 TRP B 379 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.39 ( 9090) covalent geometry : angle 0.99824 / 0.50 (12312) SS BOND : bond 0.02329 / 1.01 ( 3) SS BOND : angle 3.98788 / 2.18 ( 6) hydrogen bonds : bond 0.31836 / 21.40 ( 355) hydrogen bonds : angle 10.92478 / 7.54 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7721 (ttm) cc_final: 0.7503 (mtp) REVERT: A 230 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7601 (mtm110) REVERT: A 341 PHE cc_start: 0.7454 (m-80) cc_final: 0.7193 (m-80) REVERT: A 509 MET cc_start: 0.8156 (ttt) cc_final: 0.7923 (ttt) REVERT: A 565 LEU cc_start: 0.8828 (tt) cc_final: 0.8616 (tt) REVERT: A 636 MET cc_start: 0.8425 (tpp) cc_final: 0.8222 (mmm) REVERT: B 230 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7717 (mtm110) REVERT: B 353 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5362 (p) REVERT: B 424 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 481 MET cc_start: 0.7821 (mmm) cc_final: 0.7463 (ttt) REVERT: B 523 MET cc_start: 0.9116 (ttt) cc_final: 0.8809 (ttp) REVERT: B 605 TYR cc_start: 0.6641 (m-80) cc_final: 0.5993 (m-10) REVERT: B 636 MET cc_start: 0.8495 (tpp) cc_final: 0.8176 (mmm) outliers start: 20 outliers final: 4 residues processed: 267 average time/residue: 0.0875 time to fit residues: 32.4453 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 76 ASN A 109 ASN A 158 ASN A 267 HIS A 299 ASN A 393 GLN A 457 HIS A 583 HIS A 629 ASN B 40 HIS B 109 ASN B 126 GLN B 158 ASN B 267 HIS B 299 ASN B 393 GLN B 457 HIS B 583 HIS B 629 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126565 restraints weight = 13551.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129177 restraints weight = 8221.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130983 restraints weight = 5934.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132130 restraints weight = 4838.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132723 restraints weight = 4268.240| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9093 Z= 0.143 Angle : 0.701 10.247 12318 Z= 0.352 Chirality : 0.042 0.185 1426 Planarity : 0.004 0.030 1519 Dihedral : 6.191 57.847 1243 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.49 % Allowed : 18.36 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.20), residues: 1116 helix: -2.50 (0.17), residues: 570 sheet: -3.66 (0.62), residues: 44 loop : -3.07 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.014 0.001 TYR B 459 PHE 0.024 0.002 PHE B 117 TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9090) covalent geometry : angle 0.70039 / 0.35 (12312) SS BOND : bond 0.00300 / 0.12 ( 3) SS BOND : angle 0.94949 / 0.52 ( 6) hydrogen bonds : bond 0.04700 / 3.10 ( 355) hydrogen bonds : angle 5.47577 / 3.78 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7372 (mp0) cc_final: 0.7100 (mp0) REVERT: A 250 PHE cc_start: 0.7033 (t80) cc_final: 0.6792 (t80) REVERT: A 612 GLU cc_start: 0.7567 (mp0) cc_final: 0.7329 (mp0) REVERT: B 72 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7529 (mmmt) REVERT: B 138 GLU cc_start: 0.7939 (mp0) cc_final: 0.7552 (mp0) REVERT: B 227 LEU cc_start: 0.8865 (tt) cc_final: 0.8574 (tt) REVERT: B 230 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8236 (mtm110) REVERT: B 471 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8751 (mp) REVERT: B 523 MET cc_start: 0.9108 (ttt) cc_final: 0.8836 (ttp) REVERT: B 605 TYR cc_start: 0.6403 (m-80) cc_final: 0.6195 (m-10) outliers start: 24 outliers final: 14 residues processed: 216 average time/residue: 0.0773 time to fit residues: 24.3632 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.0030 chunk 102 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN B 109 ASN B 126 GLN B 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127235 restraints weight = 13627.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126437 restraints weight = 9217.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127175 restraints weight = 6894.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127294 restraints weight = 6122.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128828 restraints weight = 5521.140| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9093 Z= 0.175 Angle : 0.675 9.357 12318 Z= 0.338 Chirality : 0.042 0.169 1426 Planarity : 0.004 0.048 1519 Dihedral : 5.647 46.554 1241 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.63 % Allowed : 20.95 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.23), residues: 1116 helix: -1.52 (0.20), residues: 552 sheet: -3.91 (0.53), residues: 48 loop : -2.84 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.015 0.002 TYR A 276 PHE 0.024 0.002 PHE B 117 TRP 0.011 0.001 TRP B 379 HIS 0.002 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9090) covalent geometry : angle 0.67445 / 0.34 (12312) SS BOND : bond 0.00328 / 0.14 ( 3) SS BOND : angle 0.83858 / 0.48 ( 6) hydrogen bonds : bond 0.04163 / 2.76 ( 355) hydrogen bonds : angle 4.93630 / 3.40 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7929 (mp0) cc_final: 0.7619 (mp0) REVERT: A 198 MET cc_start: 0.8218 (mtp) cc_final: 0.7913 (mtp) REVERT: A 477 ASP cc_start: 0.7390 (t0) cc_final: 0.7045 (t0) REVERT: A 636 MET cc_start: 0.8541 (mtp) cc_final: 0.8163 (mtp) REVERT: B 72 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7558 (mmmt) REVERT: B 138 GLU cc_start: 0.7938 (mp0) cc_final: 0.7505 (mp0) REVERT: B 211 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: B 230 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8234 (mtm110) REVERT: B 605 TYR cc_start: 0.6559 (m-80) cc_final: 0.6331 (m-10) outliers start: 35 outliers final: 25 residues processed: 225 average time/residue: 0.0742 time to fit residues: 24.4154 Evaluate side-chains 208 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.0040 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 116 ASN A 289 ASN A 391 ASN B 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130842 restraints weight = 13678.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131323 restraints weight = 9278.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132453 restraints weight = 6863.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132356 restraints weight = 5738.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132580 restraints weight = 5104.302| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9093 Z= 0.117 Angle : 0.631 10.568 12318 Z= 0.312 Chirality : 0.041 0.184 1426 Planarity : 0.003 0.049 1519 Dihedral : 5.185 40.928 1240 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.32 % Allowed : 22.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.24), residues: 1116 helix: -1.17 (0.21), residues: 574 sheet: -3.67 (0.58), residues: 48 loop : -2.76 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.032 0.001 TYR A 518 PHE 0.024 0.002 PHE A 578 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.000 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9090) covalent geometry : angle 0.62988 / 0.31 (12312) SS BOND : bond 0.00266 / 0.12 ( 3) SS BOND : angle 1.82518 / 1.20 ( 6) hydrogen bonds : bond 0.03618 / 2.41 ( 355) hydrogen bonds : angle 4.64470 / 3.20 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 198 MET cc_start: 0.8068 (mtp) cc_final: 0.7751 (mtp) REVERT: A 252 LEU cc_start: 0.8144 (tp) cc_final: 0.7795 (tt) REVERT: A 477 ASP cc_start: 0.7490 (t0) cc_final: 0.7134 (t0) REVERT: A 565 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 585 GLU cc_start: 0.8296 (tp30) cc_final: 0.8014 (tp30) REVERT: B 72 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7603 (mmmt) REVERT: B 211 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 227 LEU cc_start: 0.8239 (tt) cc_final: 0.8017 (tt) REVERT: B 252 LEU cc_start: 0.8560 (tp) cc_final: 0.8137 (tt) REVERT: B 452 LYS cc_start: 0.8734 (tttp) cc_final: 0.7944 (ttmt) REVERT: B 470 PHE cc_start: 0.8988 (t80) cc_final: 0.8737 (t80) REVERT: B 565 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 585 GLU cc_start: 0.8579 (tp30) cc_final: 0.8332 (tp30) outliers start: 32 outliers final: 18 residues processed: 222 average time/residue: 0.0689 time to fit residues: 22.7712 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 : 0.319 ------------------------------------------------------------------------------- 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 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 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 109 ASN A 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128320 restraints weight = 13664.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128307 restraints weight = 10998.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129252 restraints weight = 7831.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129517 restraints weight = 6762.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129845 restraints weight = 5783.340| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9093 Z= 0.162 Angle : 0.649 9.693 12318 Z= 0.323 Chirality : 0.043 0.172 1426 Planarity : 0.004 0.051 1519 Dihedral : 5.031 38.755 1240 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.08 % Allowed : 20.75 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.24), residues: 1116 helix: -0.86 (0.21), residues: 574 sheet: -3.70 (0.55), residues: 48 loop : -2.76 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.017 0.002 TYR A 276 PHE 0.023 0.002 PHE B 266 TRP 0.008 0.001 TRP B 379 HIS 0.002 0.000 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 9090) covalent geometry : angle 0.64920 / 0.32 (12312) SS BOND : bond 0.00220 / 0.07 ( 3) SS BOND : angle 0.97481 / 0.62 ( 6) hydrogen bonds : bond 0.03598 / 2.37 ( 355) hydrogen bonds : angle 4.59064 / 3.15 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.263 Fit side-chains REVERT: A 40 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7942 (t-170) REVERT: A 134 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7934 (mp) REVERT: A 138 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: A 252 LEU cc_start: 0.8181 (tp) cc_final: 0.7825 (tt) REVERT: A 477 ASP cc_start: 0.7556 (t0) cc_final: 0.7202 (t0) REVERT: A 565 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8588 (tt) REVERT: A 585 GLU cc_start: 0.8362 (tp30) cc_final: 0.8134 (tp30) REVERT: B 72 LYS cc_start: 0.7835 (mmtt) cc_final: 0.7574 (mmmt) REVERT: B 211 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: B 252 LEU cc_start: 0.8557 (tp) cc_final: 0.8119 (tt) REVERT: B 565 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8762 (tt) outliers start: 49 outliers final: 33 residues processed: 221 average time/residue: 0.0665 time to fit residues: 21.9039 Evaluate side-chains 214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain 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 261 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 116 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125979 restraints weight = 13706.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125367 restraints weight = 9821.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126317 restraints weight = 7425.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126575 restraints weight = 6247.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126711 restraints weight = 5514.583| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9093 Z= 0.222 Angle : 0.725 11.026 12318 Z= 0.358 Chirality : 0.046 0.204 1426 Planarity : 0.004 0.052 1519 Dihedral : 5.256 38.992 1240 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.71 % Allowed : 20.64 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1116 helix: -0.86 (0.21), residues: 574 sheet: -3.80 (0.53), residues: 48 loop : -2.68 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 236 TYR 0.018 0.002 TYR A 276 PHE 0.023 0.002 PHE B 266 TRP 0.008 0.001 TRP A 627 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 9090) covalent geometry : angle 0.72408 / 0.36 (12312) SS BOND : bond 0.00460 / 0.17 ( 3) SS BOND : angle 1.96093 / 1.12 ( 6) hydrogen bonds : bond 0.03867 / 2.55 ( 355) hydrogen bonds : angle 4.78062 / 3.28 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 0.277 Fit side-chains REVERT: A 40 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7912 (t-170) REVERT: A 138 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 236 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7120 (mtm110) REVERT: A 477 ASP cc_start: 0.7644 (t0) cc_final: 0.7236 (t0) REVERT: A 518 TYR cc_start: 0.8480 (m-80) cc_final: 0.8214 (m-80) REVERT: A 565 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 608 CYS cc_start: 0.5077 (p) cc_final: 0.4720 (p) REVERT: B 72 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7572 (mmmt) REVERT: B 211 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: B 458 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: B 565 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8747 (tt) outliers start: 55 outliers final: 36 residues processed: 223 average time/residue: 0.0682 time to fit residues: 22.6832 Evaluate side-chains 223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 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 A residue 592 CYS Chi-restraints excluded: chain B residue 37 LEU 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 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 471 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129796 restraints weight = 13673.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129089 restraints weight = 8649.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129860 restraints weight = 7155.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130329 restraints weight = 5954.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130475 restraints weight = 5195.198| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9093 Z= 0.125 Angle : 0.657 10.668 12318 Z= 0.320 Chirality : 0.043 0.308 1426 Planarity : 0.004 0.053 1519 Dihedral : 4.967 36.997 1240 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.39 % Allowed : 20.54 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.25), residues: 1116 helix: -0.66 (0.22), residues: 574 sheet: -3.50 (0.54), residues: 48 loop : -2.60 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.019 0.001 TYR A 276 PHE 0.024 0.002 PHE A 266 TRP 0.007 0.001 TRP B 627 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9090) covalent geometry : angle 0.65574 / 0.32 (12312) SS BOND : bond 0.00145 / 0.07 ( 3) SS BOND : angle 1.58375 / 1.00 ( 6) hydrogen bonds : bond 0.03447 / 2.29 ( 355) hydrogen bonds : angle 4.66306 / 3.19 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 138 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 154 ASN cc_start: 0.7999 (t0) cc_final: 0.7797 (t0) REVERT: A 424 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 565 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 72 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7511 (mmmt) REVERT: B 107 LEU cc_start: 0.8251 (tp) cc_final: 0.7916 (tp) REVERT: B 154 ASN cc_start: 0.7996 (t0) cc_final: 0.7702 (m-40) REVERT: B 211 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 458 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: B 473 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8573 (mtpt) REVERT: B 565 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8729 (tt) outliers start: 52 outliers final: 32 residues processed: 230 average time/residue: 0.0753 time to fit residues: 25.5792 Evaluate side-chains 225 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 225 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127230 restraints weight = 13524.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127018 restraints weight = 8578.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127541 restraints weight = 7933.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127780 restraints weight = 6333.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127972 restraints weight = 5636.504| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9093 Z= 0.193 Angle : 0.738 10.078 12318 Z= 0.363 Chirality : 0.046 0.293 1426 Planarity : 0.004 0.056 1519 Dihedral : 5.119 36.739 1240 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.56 % Allowed : 21.37 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.25), residues: 1116 helix: -0.72 (0.21), residues: 580 sheet: -3.34 (0.55), residues: 48 loop : -2.53 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 236 TYR 0.033 0.002 TYR A 518 PHE 0.025 0.002 PHE B 266 TRP 0.008 0.001 TRP B 627 HIS 0.002 0.000 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 9090) covalent geometry : angle 0.73699 / 0.36 (12312) SS BOND : bond 0.00351 / 0.16 ( 3) SS BOND : angle 2.06288 / 1.21 ( 6) hydrogen bonds : bond 0.03719 / 2.46 ( 355) hydrogen bonds : angle 4.72429 / 3.22 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.323 Fit side-chains REVERT: A 134 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 138 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 424 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 454 LEU cc_start: 0.8788 (tt) cc_final: 0.8532 (tp) REVERT: A 565 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 608 CYS cc_start: 0.4890 (p) cc_final: 0.4566 (p) REVERT: B 72 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7455 (mmmt) REVERT: B 107 LEU cc_start: 0.8237 (tp) cc_final: 0.7948 (tp) REVERT: B 154 ASN cc_start: 0.8057 (t0) cc_final: 0.7739 (m-40) REVERT: B 211 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 458 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: B 565 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 585 GLU cc_start: 0.8704 (tp30) cc_final: 0.8496 (tp30) outliers start: 44 outliers final: 35 residues processed: 214 average time/residue: 0.0666 time to fit residues: 21.7011 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 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 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 471 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN A 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128853 restraints weight = 13429.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129184 restraints weight = 9037.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129867 restraints weight = 6328.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130018 restraints weight = 5608.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130405 restraints weight = 5252.957| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9093 Z= 0.129 Angle : 0.697 11.500 12318 Z= 0.340 Chirality : 0.043 0.264 1426 Planarity : 0.004 0.059 1519 Dihedral : 4.949 37.263 1240 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.25), residues: 1116 helix: -0.53 (0.22), residues: 562 sheet: -2.69 (0.62), residues: 44 loop : -2.46 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 236 TYR 0.027 0.001 TYR A 518 PHE 0.025 0.002 PHE B 250 TRP 0.007 0.001 TRP B 627 HIS 0.013 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9090) covalent geometry : angle 0.69574 / 0.34 (12312) SS BOND : bond 0.00350 / 0.14 ( 3) SS BOND : angle 2.08397 / 1.18 ( 6) hydrogen bonds : bond 0.03450 / 2.30 ( 355) hydrogen bonds : angle 4.65491 / 3.18 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7944 (mp) REVERT: A 138 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 458 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 565 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 608 CYS cc_start: 0.4801 (p) cc_final: 0.4541 (p) REVERT: B 72 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7418 (mmmt) REVERT: B 107 LEU cc_start: 0.8222 (tp) cc_final: 0.7945 (tp) REVERT: B 211 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 458 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: B 477 ASP cc_start: 0.7225 (t70) cc_final: 0.6737 (t0) REVERT: B 565 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 585 GLU cc_start: 0.8608 (tp30) cc_final: 0.7939 (tp30) outliers start: 42 outliers final: 32 residues processed: 225 average time/residue: 0.0671 time to fit residues: 22.8698 Evaluate side-chains 231 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 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 226 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 471 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 66 optimal weight: 0.0010 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130423 restraints weight = 13398.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130664 restraints weight = 8471.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131001 restraints weight = 6111.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131337 restraints weight = 6191.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131607 restraints weight = 5396.005| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9093 Z= 0.120 Angle : 0.690 11.759 12318 Z= 0.335 Chirality : 0.043 0.256 1426 Planarity : 0.004 0.062 1519 Dihedral : 4.880 36.798 1240 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.73 % Allowed : 22.20 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.25), residues: 1116 helix: -0.44 (0.22), residues: 562 sheet: -2.26 (0.68), residues: 44 loop : -2.46 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 236 TYR 0.025 0.001 TYR A 518 PHE 0.020 0.002 PHE A 591 TRP 0.006 0.001 TRP A 627 HIS 0.010 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9090) covalent geometry : angle 0.68964 / 0.33 (12312) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 1.35620 / 0.85 ( 6) hydrogen bonds : bond 0.03359 / 2.24 ( 355) hydrogen bonds : angle 4.60173 / 3.14 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 138 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 458 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: A 565 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8742 (tt) REVERT: B 72 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7402 (mmmt) REVERT: B 107 LEU cc_start: 0.8213 (tp) cc_final: 0.7922 (tp) REVERT: B 154 ASN cc_start: 0.8114 (t0) cc_final: 0.7822 (m110) REVERT: B 211 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 452 LYS cc_start: 0.8753 (tttm) cc_final: 0.8484 (tttm) REVERT: B 458 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: B 477 ASP cc_start: 0.7332 (t70) cc_final: 0.6949 (t0) REVERT: B 565 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 585 GLU cc_start: 0.8588 (tp30) cc_final: 0.7973 (tp30) outliers start: 36 outliers final: 26 residues processed: 221 average time/residue: 0.0669 time to fit residues: 22.3188 Evaluate side-chains 223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 458 GLU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 584 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 6.9990 chunk 50 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130490 restraints weight = 13223.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131057 restraints weight = 8747.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132145 restraints weight = 6373.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132145 restraints weight = 5237.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132227 restraints weight = 4928.055| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9093 Z= 0.136 Angle : 0.711 11.768 12318 Z= 0.344 Chirality : 0.044 0.282 1426 Planarity : 0.004 0.071 1519 Dihedral : 4.849 36.650 1240 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.94 % Allowed : 22.82 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.25), residues: 1116 helix: -0.42 (0.22), residues: 562 sheet: -2.17 (0.69), residues: 44 loop : -2.45 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 236 TYR 0.023 0.001 TYR A 518 PHE 0.026 0.002 PHE B 250 TRP 0.006 0.001 TRP A 627 HIS 0.009 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9090) covalent geometry : angle 0.71045 / 0.34 (12312) SS BOND : bond 0.00180 / 0.09 ( 3) SS BOND : angle 1.79582 / 1.15 ( 6) hydrogen bonds : bond 0.03424 / 2.30 ( 355) hydrogen bonds : angle 4.54647 / 3.12 ( 1017) =============================================================================== Job complete usr+sys time: 1347.29 seconds wall clock time: 24 minutes 8.29 seconds (1448.29 seconds total)