Starting phenix.real_space_refine on Fri Sep 11 10:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxj_21440/09_2026/6vxj_21440.cif" } resolution = 4.1 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= 0.014 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 1454 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 8895 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'CLR': 1, 'RS4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.06, per 1000 atoms: 0.23 Number of scatterers: 8895 At special positions: 0 Unit cell: (104.55, 77.49, 126.69, 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 1589 8.00 N 1454 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=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 1.02 Conformation dependent library (CDL) restraints added in 385.1 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: 52 helices and 4 sheets defined 54.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.652A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.629A pdb=" N ASN A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 removed outlier: 4.164A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 5.084A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.528A pdb=" N THR A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.280A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.978A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.215A 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 Processing helix chain 'A' and resid 330 through 336 removed outlier: 4.185A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.717A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 removed outlier: 3.727A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 removed outlier: 3.678A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 440 removed outlier: 4.027A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.519A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.849A pdb=" N GLU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.583A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 4.174A pdb=" N CYS A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 527 removed outlier: 3.500A pdb=" N PHE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 4.082A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.570A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.224A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.514A pdb=" N VAL A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 650 removed outlier: 3.615A pdb=" N LEU A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 639 " --> pdb=" O CYS A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.652A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.629A pdb=" N ASN B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 4.165A pdb=" N SER B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 5.084A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.529A pdb=" N THR B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 4.281A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.978A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.215A 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 Processing helix chain 'B' and resid 330 through 336 removed outlier: 4.185A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 352 removed outlier: 3.718A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 389 removed outlier: 3.726A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 413 removed outlier: 3.679A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 440 removed outlier: 4.027A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.519A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.849A pdb=" N GLU B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 478 removed outlier: 3.583A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 4.174A pdb=" N CYS B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 527 removed outlier: 3.641A pdb=" N MET B 514 " --> pdb=" O MET B 510 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 4.080A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.570A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 572 through 584 removed outlier: 4.224A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.514A pdb=" N VAL B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 650 removed outlier: 3.616A pdb=" N LEU B 626 " --> pdb=" O SER B 622 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 639 " --> pdb=" O CYS B 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 6.818A pdb=" N SER A 65 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS A 43 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.655A 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: 6.309A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.024A 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: 6.817A pdb=" N SER B 65 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS B 43 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.655A 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: 6.309A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 75 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1059 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: 1.69 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2621 1.34 - 1.45: 1656 1.45 - 1.57: 4718 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9089 Sorted by residual: bond pdb=" C28 RS4 B 701 " pdb=" O29 RS4 B 701 " ideal model delta sigma weight residual 1.324 1.444 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C10 RS4 B 701 " pdb=" C9 RS4 B 701 " ideal model delta sigma weight residual 1.367 1.478 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C20 RS4 B 701 " pdb=" C21 RS4 B 701 " ideal model delta sigma weight residual 1.365 1.474 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C LEU B 479 " pdb=" N PRO B 480 " ideal model delta sigma weight residual 1.337 1.375 -0.038 1.06e-02 8.90e+03 1.32e+01 bond pdb=" C LEU A 479 " pdb=" N PRO A 480 " ideal model delta sigma weight residual 1.337 1.375 -0.038 1.06e-02 8.90e+03 1.31e+01 ... (remaining 9084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11531 1.88 - 3.77: 661 3.77 - 5.65: 94 5.65 - 7.54: 22 7.54 - 9.42: 10 Bond angle restraints: 12318 Sorted by residual: angle pdb=" N PRO B 485 " pdb=" CA PRO B 485 " pdb=" C PRO B 485 " ideal model delta sigma weight residual 114.68 108.93 5.75 1.28e+00 6.10e-01 2.02e+01 angle pdb=" N PRO A 485 " pdb=" CA PRO A 485 " pdb=" C PRO A 485 " ideal model delta sigma weight residual 114.68 108.93 5.75 1.28e+00 6.10e-01 2.02e+01 angle pdb=" C ASN A 557 " pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C ASN B 557 " pdb=" N LEU B 558 " pdb=" CA LEU B 558 " ideal model delta sigma weight residual 121.54 128.67 -7.13 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 ... (remaining 12313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4650 16.99 - 33.98: 520 33.98 - 50.97: 154 50.97 - 67.96: 38 67.96 - 84.95: 12 Dihedral angle restraints: 5374 sinusoidal: 2114 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 8.05 84.95 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CA LEU B 484 " pdb=" C LEU B 484 " pdb=" N PRO B 485 " pdb=" CA PRO B 485 " ideal model delta harmonic sigma weight residual 180.00 137.76 42.24 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA LEU A 484 " pdb=" C LEU A 484 " pdb=" N PRO A 485 " pdb=" CA PRO A 485 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 ... (remaining 5371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1061 0.058 - 0.116: 308 0.116 - 0.173: 52 0.173 - 0.231: 3 0.231 - 0.289: 3 Chirality restraints: 1427 Sorted by residual: 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 -2.64 -0.29 2.00e-01 2.50e+01 2.09e+00 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=" C14 CLR A 701 " pdb=" C13 CLR A 701 " pdb=" C15 CLR A 701 " pdb=" C8 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1424 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 484 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 485 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 485 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 378 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ARG A 378 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG A 378 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 379 " -0.010 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2348 2.78 - 3.31: 8136 3.31 - 3.84: 14661 3.84 - 4.37: 17074 4.37 - 4.90: 28878 Nonbonded interactions: 71097 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.252 3.040 nonbonded pdb=" N ASN B 338 " pdb=" OD1 ASN B 338 " model vdw 2.267 3.120 nonbonded pdb=" N ASN A 338 " pdb=" OD1 ASN A 338 " model vdw 2.267 3.120 nonbonded pdb=" O LEU A 146 " pdb=" OG1 THR A 371 " model vdw 2.280 3.040 ... (remaining 71092 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.007 0.120 9092 Z= 0.336 Angle : 1.017 9.420 12324 Z= 0.548 Chirality : 0.055 0.289 1427 Planarity : 0.006 0.084 1522 Dihedral : 16.267 83.686 3273 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.32 % Allowed : 10.17 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -5.74 (0.17), residues: 1116 helix: -4.22 (0.09), residues: 616 sheet: -1.30 (0.85), residues: 34 loop : -3.22 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 137 TYR 0.012 0.002 TYR A 613 PHE 0.019 0.002 PHE A 489 TRP 0.013 0.002 TRP B 627 HIS 0.003 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.34 ( 9089) covalent geometry : angle 1.01654 / 0.55 (12318) SS BOND : bond 0.00337 / 0.15 ( 3) SS BOND : angle 2.00193 / 1.04 ( 6) hydrogen bonds : bond 0.30596 / 20.39 ( 365) hydrogen bonds : angle 10.37537 / 7.29 ( 1059) *********************** 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 357 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.7228 (p0) cc_final: 0.6888 (p0) REVERT: A 86 LYS cc_start: 0.8539 (tttt) cc_final: 0.8250 (ttpt) REVERT: A 143 SER cc_start: 0.7685 (p) cc_final: 0.7375 (p) REVERT: A 172 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8627 (ttmt) REVERT: A 192 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8448 (mmtm) REVERT: A 240 PHE cc_start: 0.8278 (p90) cc_final: 0.7782 (p90) REVERT: A 265 MET cc_start: 0.7324 (mmt) cc_final: 0.6997 (tpp) REVERT: A 266 PHE cc_start: 0.8114 (t80) cc_final: 0.7674 (t80) REVERT: A 277 PHE cc_start: 0.6539 (m-80) cc_final: 0.6213 (m-80) REVERT: A 336 TYR cc_start: 0.8117 (t80) cc_final: 0.7728 (t80) REVERT: A 423 ILE cc_start: 0.9336 (mp) cc_final: 0.9086 (tp) REVERT: A 430 LEU cc_start: 0.9330 (mt) cc_final: 0.9126 (mt) REVERT: A 470 PHE cc_start: 0.8828 (t80) cc_final: 0.8621 (t80) REVERT: A 514 MET cc_start: 0.8620 (ptp) cc_final: 0.8209 (ptt) REVERT: A 518 TYR cc_start: 0.9095 (m-10) cc_final: 0.8891 (m-80) REVERT: A 533 VAL cc_start: 0.8838 (m) cc_final: 0.8625 (t) REVERT: A 548 MET cc_start: 0.8262 (mtt) cc_final: 0.7410 (mtm) REVERT: A 565 LEU cc_start: 0.9241 (tp) cc_final: 0.9009 (tp) REVERT: A 573 ILE cc_start: 0.9082 (mt) cc_final: 0.8652 (mt) REVERT: A 617 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8138 (mm-40) REVERT: A 629 ASN cc_start: 0.9001 (m-40) cc_final: 0.8615 (m-40) REVERT: A 652 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8397 (tttt) REVERT: B 68 ASN cc_start: 0.7211 (p0) cc_final: 0.6828 (p0) REVERT: B 86 LYS cc_start: 0.8046 (tttt) cc_final: 0.7826 (ttpt) REVERT: B 137 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7789 (ttm110) REVERT: B 143 SER cc_start: 0.8117 (p) cc_final: 0.7793 (p) REVERT: B 198 MET cc_start: 0.9079 (ttm) cc_final: 0.8700 (ttm) REVERT: B 266 PHE cc_start: 0.8268 (t80) cc_final: 0.7823 (t80) REVERT: B 277 PHE cc_start: 0.6249 (m-80) cc_final: 0.5995 (m-80) REVERT: B 336 TYR cc_start: 0.8030 (t80) cc_final: 0.7551 (t80) REVERT: B 477 ASP cc_start: 0.7927 (t0) cc_final: 0.7632 (t0) REVERT: B 502 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8165 (ttmt) REVERT: B 514 MET cc_start: 0.8602 (ptp) cc_final: 0.8053 (ptt) REVERT: B 523 MET cc_start: 0.8852 (tpt) cc_final: 0.8637 (tpt) REVERT: B 548 MET cc_start: 0.8375 (mtt) cc_final: 0.7730 (mtm) REVERT: B 573 ILE cc_start: 0.9234 (mt) cc_final: 0.8765 (mp) REVERT: B 585 GLU cc_start: 0.8825 (tp30) cc_final: 0.8493 (mm-30) REVERT: B 605 TYR cc_start: 0.5858 (m-80) cc_final: 0.5302 (m-80) REVERT: B 629 ASN cc_start: 0.8955 (m-40) cc_final: 0.8475 (m-40) REVERT: B 630 HIS cc_start: 0.8544 (m170) cc_final: 0.8249 (m170) REVERT: B 636 MET cc_start: 0.8252 (tpp) cc_final: 0.7997 (tpp) REVERT: B 646 LEU cc_start: 0.8227 (tt) cc_final: 0.7672 (mm) REVERT: B 650 PHE cc_start: 0.7850 (m-80) cc_final: 0.7629 (m-10) outliers start: 32 outliers final: 9 residues processed: 339 average time/residue: 0.0986 time to fit residues: 45.7030 Evaluate side-chains 249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 238 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 68 ASN A 76 ASN A 109 ASN A 120 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 289 ASN A 398 GLN A 425 ASN A 437 GLN A 583 HIS A 601 ASN A 629 ASN A 630 HIS B 40 HIS B 76 ASN B 109 ASN B 120 ASN B 289 ASN B 425 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN B 583 HIS B 601 ASN B 629 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117587 restraints weight = 16701.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120723 restraints weight = 9951.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122764 restraints weight = 6958.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123969 restraints weight = 5479.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124906 restraints weight = 4707.105| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9092 Z= 0.161 Angle : 0.663 6.547 12324 Z= 0.341 Chirality : 0.041 0.177 1427 Planarity : 0.005 0.072 1522 Dihedral : 6.051 59.179 1255 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.31 % Allowed : 4.88 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -3.88 (0.21), residues: 1116 helix: -2.19 (0.17), residues: 624 sheet: -1.32 (0.73), residues: 34 loop : -3.13 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.014 0.002 TYR B 494 PHE 0.019 0.002 PHE B 489 TRP 0.006 0.001 TRP B 379 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9089) covalent geometry : angle 0.66239 / 0.34 (12318) SS BOND : bond 0.00308 / 0.14 ( 3) SS BOND : angle 1.00291 / 0.64 ( 6) hydrogen bonds : bond 0.04483 / 3.15 ( 365) hydrogen bonds : angle 5.27522 / 3.72 ( 1059) *********************** 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 302 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8379 (tttt) cc_final: 0.8101 (ttpt) REVERT: A 143 SER cc_start: 0.7548 (p) cc_final: 0.7195 (p) REVERT: A 192 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8615 (mmmm) REVERT: A 196 ILE cc_start: 0.8947 (mt) cc_final: 0.8712 (mm) REVERT: A 240 PHE cc_start: 0.8701 (p90) cc_final: 0.8165 (p90) REVERT: A 266 PHE cc_start: 0.8363 (t80) cc_final: 0.7943 (t80) REVERT: A 277 PHE cc_start: 0.6318 (m-80) cc_final: 0.5894 (m-80) REVERT: A 377 LEU cc_start: 0.9111 (mm) cc_final: 0.8897 (mt) REVERT: A 470 PHE cc_start: 0.8694 (t80) cc_final: 0.8152 (t80) REVERT: A 514 MET cc_start: 0.8265 (ptp) cc_final: 0.7859 (ptt) REVERT: A 557 ASN cc_start: 0.8019 (t0) cc_final: 0.7441 (m-40) REVERT: A 565 LEU cc_start: 0.8905 (tp) cc_final: 0.8655 (tp) REVERT: A 617 GLN cc_start: 0.8708 (mm-40) cc_final: 0.7905 (mm-40) REVERT: A 629 ASN cc_start: 0.8851 (m110) cc_final: 0.8600 (m-40) REVERT: B 71 MET cc_start: 0.7919 (mmm) cc_final: 0.7109 (mmm) REVERT: B 143 SER cc_start: 0.8032 (p) cc_final: 0.7699 (p) REVERT: B 160 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7828 (tpt170) REVERT: B 198 MET cc_start: 0.8925 (ttm) cc_final: 0.8482 (ttm) REVERT: B 253 PHE cc_start: 0.7471 (m-80) cc_final: 0.7241 (m-80) REVERT: B 514 MET cc_start: 0.8357 (ptp) cc_final: 0.7845 (ptt) REVERT: B 548 MET cc_start: 0.8114 (mtt) cc_final: 0.7817 (mtt) outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.0791 time to fit residues: 34.3127 Evaluate side-chains 233 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 283 HIS A 457 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114252 restraints weight = 16783.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116866 restraints weight = 10436.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118707 restraints weight = 7541.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119906 restraints weight = 6052.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120507 restraints weight = 5243.406| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9092 Z= 0.212 Angle : 0.689 10.839 12324 Z= 0.351 Chirality : 0.042 0.142 1427 Planarity : 0.005 0.070 1522 Dihedral : 5.995 56.204 1255 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -3.02 (0.23), residues: 1116 helix: -1.22 (0.19), residues: 608 sheet: -1.25 (0.78), residues: 34 loop : -3.13 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 163 TYR 0.018 0.002 TYR A 494 PHE 0.021 0.002 PHE B 385 TRP 0.008 0.001 TRP A 379 HIS 0.011 0.002 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 ( 9089) covalent geometry : angle 0.68924 / 0.35 (12318) SS BOND : bond 0.00777 / 0.34 ( 3) SS BOND : angle 0.86169 / 0.55 ( 6) hydrogen bonds : bond 0.04004 / 2.79 ( 365) hydrogen bonds : angle 4.97697 / 3.49 ( 1059) *********************** 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 291 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7909 (mmt) cc_final: 0.7378 (mmm) REVERT: A 81 PRO cc_start: 0.8419 (Cg_endo) cc_final: 0.7807 (Cg_exo) REVERT: A 86 LYS cc_start: 0.8524 (tttt) cc_final: 0.8196 (ttpt) REVERT: A 143 SER cc_start: 0.7902 (p) cc_final: 0.7686 (p) REVERT: A 192 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8476 (mmmm) REVERT: A 240 PHE cc_start: 0.8821 (p90) cc_final: 0.8417 (p90) REVERT: A 266 PHE cc_start: 0.8379 (t80) cc_final: 0.8103 (t80) REVERT: A 276 TYR cc_start: 0.7976 (t80) cc_final: 0.7314 (t80) REVERT: A 277 PHE cc_start: 0.6535 (m-80) cc_final: 0.6071 (m-80) REVERT: A 442 VAL cc_start: 0.8919 (t) cc_final: 0.8638 (t) REVERT: A 458 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 470 PHE cc_start: 0.8885 (t80) cc_final: 0.8662 (t80) REVERT: A 490 THR cc_start: 0.8546 (p) cc_final: 0.7825 (p) REVERT: A 557 ASN cc_start: 0.8249 (t0) cc_final: 0.7856 (m-40) REVERT: A 565 LEU cc_start: 0.9109 (tp) cc_final: 0.8889 (tp) REVERT: A 617 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8039 (mm-40) REVERT: A 629 ASN cc_start: 0.8997 (m110) cc_final: 0.8441 (m-40) REVERT: B 71 MET cc_start: 0.7877 (mmm) cc_final: 0.6928 (mmm) REVERT: B 81 PRO cc_start: 0.8013 (Cg_endo) cc_final: 0.7792 (Cg_exo) REVERT: B 96 ARG cc_start: 0.7905 (mmt90) cc_final: 0.7289 (mmm-85) REVERT: B 143 SER cc_start: 0.8259 (p) cc_final: 0.8058 (p) REVERT: B 160 ARG cc_start: 0.8715 (ttm110) cc_final: 0.7824 (tpt170) REVERT: B 265 MET cc_start: 0.7898 (ttm) cc_final: 0.7593 (ttp) REVERT: B 424 GLN cc_start: 0.6825 (tt0) cc_final: 0.6544 (mt0) REVERT: B 460 ILE cc_start: 0.9087 (tp) cc_final: 0.8719 (tp) REVERT: B 470 PHE cc_start: 0.9055 (t80) cc_final: 0.8820 (t80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.0757 time to fit residues: 32.0860 Evaluate side-chains 233 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115144 restraints weight = 16947.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117964 restraints weight = 10109.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120208 restraints weight = 7090.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121276 restraints weight = 5592.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122261 restraints weight = 4832.450| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9092 Z= 0.169 Angle : 0.646 8.863 12324 Z= 0.324 Chirality : 0.042 0.141 1427 Planarity : 0.005 0.073 1522 Dihedral : 5.867 54.639 1255 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -2.61 (0.24), residues: 1116 helix: -0.75 (0.20), residues: 592 sheet: -1.28 (0.77), residues: 34 loop : -3.06 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 163 TYR 0.018 0.002 TYR A 464 PHE 0.021 0.002 PHE B 385 TRP 0.009 0.001 TRP B 624 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9089) covalent geometry : angle 0.64614 / 0.32 (12318) SS BOND : bond 0.00297 / 0.14 ( 3) SS BOND : angle 1.15050 / 0.66 ( 6) hydrogen bonds : bond 0.03498 / 2.45 ( 365) hydrogen bonds : angle 4.85198 / 3.40 ( 1059) *********************** 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 279 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PRO cc_start: 0.8348 (Cg_endo) cc_final: 0.7958 (Cg_exo) REVERT: A 86 LYS cc_start: 0.8483 (tttt) cc_final: 0.8232 (ttpt) REVERT: A 141 GLN cc_start: 0.8306 (mp-120) cc_final: 0.7840 (mp10) REVERT: A 192 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8567 (mmmm) REVERT: A 240 PHE cc_start: 0.8742 (p90) cc_final: 0.8325 (p90) REVERT: A 266 PHE cc_start: 0.8409 (t80) cc_final: 0.7987 (t80) REVERT: A 276 TYR cc_start: 0.8023 (t80) cc_final: 0.7271 (t80) REVERT: A 277 PHE cc_start: 0.6451 (m-80) cc_final: 0.5991 (m-80) REVERT: A 346 LYS cc_start: 0.7586 (tptp) cc_final: 0.7265 (mtpp) REVERT: A 458 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 470 PHE cc_start: 0.8856 (t80) cc_final: 0.8601 (t80) REVERT: A 490 THR cc_start: 0.8402 (p) cc_final: 0.7837 (p) REVERT: A 514 MET cc_start: 0.8006 (ptp) cc_final: 0.7700 (ptt) REVERT: A 557 ASN cc_start: 0.8300 (t0) cc_final: 0.7783 (m-40) REVERT: A 617 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7924 (mm-40) REVERT: A 629 ASN cc_start: 0.8879 (m110) cc_final: 0.8297 (m-40) REVERT: B 71 MET cc_start: 0.7831 (mmm) cc_final: 0.6994 (mmm) REVERT: B 96 ARG cc_start: 0.7831 (mmt90) cc_final: 0.7258 (mmm-85) REVERT: B 160 ARG cc_start: 0.8643 (ttm110) cc_final: 0.7803 (tpt-90) REVERT: B 342 TYR cc_start: 0.7257 (t80) cc_final: 0.6606 (t80) REVERT: B 424 GLN cc_start: 0.6772 (tt0) cc_final: 0.6477 (mt0) REVERT: B 430 LEU cc_start: 0.9454 (mt) cc_final: 0.9227 (mt) REVERT: B 460 ILE cc_start: 0.9129 (tp) cc_final: 0.8685 (tp) REVERT: B 604 ASN cc_start: 0.7584 (p0) cc_final: 0.7307 (p0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.0786 time to fit residues: 31.6460 Evaluate side-chains 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 283 HIS A 630 HIS B 40 HIS B 41 ASN B 222 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115566 restraints weight = 16901.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118253 restraints weight = 10373.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120135 restraints weight = 7408.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121126 restraints weight = 5906.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122071 restraints weight = 5149.125| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9092 Z= 0.170 Angle : 0.647 6.452 12324 Z= 0.326 Chirality : 0.042 0.165 1427 Planarity : 0.004 0.068 1522 Dihedral : 5.792 54.001 1255 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -2.42 (0.24), residues: 1116 helix: -0.75 (0.20), residues: 602 sheet: -1.38 (0.76), residues: 34 loop : -2.75 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 163 TYR 0.022 0.002 TYR A 494 PHE 0.022 0.002 PHE B 489 TRP 0.011 0.001 TRP B 624 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9089) covalent geometry : angle 0.64714 / 0.33 (12318) SS BOND : bond 0.00387 / 0.18 ( 3) SS BOND : angle 1.14457 / 0.66 ( 6) hydrogen bonds : bond 0.03365 / 2.36 ( 365) hydrogen bonds : angle 4.80202 / 3.37 ( 1059) *********************** 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 280 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PRO cc_start: 0.8321 (Cg_endo) cc_final: 0.7969 (Cg_exo) REVERT: A 86 LYS cc_start: 0.8561 (tttt) cc_final: 0.8339 (ttpt) REVERT: A 187 SER cc_start: 0.8099 (m) cc_final: 0.7684 (p) REVERT: A 192 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8747 (mmmm) REVERT: A 240 PHE cc_start: 0.8787 (p90) cc_final: 0.8375 (p90) REVERT: A 266 PHE cc_start: 0.8313 (t80) cc_final: 0.8000 (t80) REVERT: A 276 TYR cc_start: 0.8027 (t80) cc_final: 0.7228 (t80) REVERT: A 277 PHE cc_start: 0.6510 (m-80) cc_final: 0.6012 (m-80) REVERT: A 346 LYS cc_start: 0.7572 (tptp) cc_final: 0.7250 (mtpp) REVERT: A 442 VAL cc_start: 0.8782 (t) cc_final: 0.8577 (t) REVERT: A 458 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7610 (mm-30) REVERT: A 490 THR cc_start: 0.8441 (p) cc_final: 0.7766 (p) REVERT: A 514 MET cc_start: 0.8145 (ptp) cc_final: 0.7753 (ptt) REVERT: A 548 MET cc_start: 0.8097 (mtt) cc_final: 0.7552 (mtm) REVERT: A 557 ASN cc_start: 0.8298 (t0) cc_final: 0.7790 (m-40) REVERT: A 573 ILE cc_start: 0.9352 (mt) cc_final: 0.9096 (mt) REVERT: A 617 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7963 (mm-40) REVERT: A 629 ASN cc_start: 0.8855 (m110) cc_final: 0.8266 (m-40) REVERT: B 71 MET cc_start: 0.7847 (mmm) cc_final: 0.6837 (mmm) REVERT: B 96 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7319 (mmm-85) REVERT: B 105 ASP cc_start: 0.7500 (t0) cc_final: 0.7217 (p0) REVERT: B 152 MET cc_start: 0.6678 (ptp) cc_final: 0.6287 (ptp) REVERT: B 160 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8005 (tpt-90) REVERT: B 199 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6694 (mm-30) REVERT: B 342 TYR cc_start: 0.7467 (t80) cc_final: 0.6966 (t80) REVERT: B 424 GLN cc_start: 0.6594 (tt0) cc_final: 0.6320 (mt0) REVERT: B 430 LEU cc_start: 0.9456 (mt) cc_final: 0.9249 (mt) REVERT: B 458 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 460 ILE cc_start: 0.9114 (tp) cc_final: 0.8833 (tp) REVERT: B 604 ASN cc_start: 0.7645 (p0) cc_final: 0.7353 (p0) REVERT: B 629 ASN cc_start: 0.8925 (m110) cc_final: 0.8357 (m-40) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.0761 time to fit residues: 31.1287 Evaluate side-chains 237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 64 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 283 HIS A 630 HIS B 40 HIS B 141 GLN B 387 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119087 restraints weight = 16924.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121914 restraints weight = 10266.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123767 restraints weight = 7304.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124803 restraints weight = 5830.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125829 restraints weight = 5058.528| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9092 Z= 0.115 Angle : 0.616 7.052 12324 Z= 0.303 Chirality : 0.041 0.157 1427 Planarity : 0.004 0.061 1522 Dihedral : 5.537 52.128 1255 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.10 % Allowed : 0.83 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -2.26 (0.24), residues: 1116 helix: -0.50 (0.21), residues: 590 sheet: -0.91 (0.78), residues: 34 loop : -2.85 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 482 TYR 0.013 0.001 TYR B 464 PHE 0.023 0.002 PHE B 385 TRP 0.009 0.001 TRP B 624 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9089) covalent geometry : angle 0.61558 / 0.30 (12318) SS BOND : bond 0.00565 / 0.24 ( 3) SS BOND : angle 1.06004 / 0.66 ( 6) hydrogen bonds : bond 0.03135 / 2.15 ( 365) hydrogen bonds : angle 4.60299 / 3.22 ( 1059) *********************** 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 283 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PRO cc_start: 0.8327 (Cg_endo) cc_final: 0.7993 (Cg_exo) REVERT: A 105 ASP cc_start: 0.7891 (t70) cc_final: 0.7641 (t0) REVERT: A 119 CYS cc_start: 0.7080 (t) cc_final: 0.6740 (t) REVERT: A 120 ASN cc_start: 0.8139 (p0) cc_final: 0.7347 (m-40) REVERT: A 131 MET cc_start: 0.7765 (mmm) cc_final: 0.7210 (mmm) REVERT: A 141 GLN cc_start: 0.8356 (mp-120) cc_final: 0.7882 (mp10) REVERT: A 143 SER cc_start: 0.7940 (p) cc_final: 0.7736 (p) REVERT: A 187 SER cc_start: 0.8122 (m) cc_final: 0.7702 (p) REVERT: A 192 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8780 (mmmm) REVERT: A 238 ILE cc_start: 0.9082 (mp) cc_final: 0.8747 (mp) REVERT: A 240 PHE cc_start: 0.8710 (p90) cc_final: 0.8216 (p90) REVERT: A 265 MET cc_start: 0.7195 (mmm) cc_final: 0.6979 (mmm) REVERT: A 276 TYR cc_start: 0.8062 (t80) cc_final: 0.7356 (t80) REVERT: A 277 PHE cc_start: 0.6728 (m-80) cc_final: 0.6241 (m-80) REVERT: A 346 LYS cc_start: 0.7651 (tptp) cc_final: 0.7320 (mtpp) REVERT: A 458 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 514 MET cc_start: 0.8101 (ptp) cc_final: 0.7720 (ptt) REVERT: A 523 MET cc_start: 0.8708 (tmm) cc_final: 0.8498 (tmm) REVERT: A 557 ASN cc_start: 0.8323 (t0) cc_final: 0.7729 (m-40) REVERT: A 617 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7866 (mm-40) REVERT: B 71 MET cc_start: 0.7653 (mmm) cc_final: 0.6755 (mmm) REVERT: B 96 ARG cc_start: 0.7934 (mmt90) cc_final: 0.7353 (mmm-85) REVERT: B 105 ASP cc_start: 0.7546 (t0) cc_final: 0.7259 (t0) REVERT: B 152 MET cc_start: 0.6504 (ptp) cc_final: 0.6225 (ptp) REVERT: B 160 ARG cc_start: 0.8808 (ttm110) cc_final: 0.7930 (tpt-90) REVERT: B 199 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 276 TYR cc_start: 0.7735 (t80) cc_final: 0.7144 (t80) REVERT: B 277 PHE cc_start: 0.6384 (m-80) cc_final: 0.5986 (m-80) REVERT: B 342 TYR cc_start: 0.7425 (t80) cc_final: 0.7087 (t80) REVERT: B 424 GLN cc_start: 0.6594 (tt0) cc_final: 0.6367 (mt0) REVERT: B 458 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 514 MET cc_start: 0.8068 (ptp) cc_final: 0.7510 (ptt) REVERT: B 548 MET cc_start: 0.7988 (mtt) cc_final: 0.7663 (ttm) REVERT: B 573 ILE cc_start: 0.9138 (mt) cc_final: 0.8713 (mt) REVERT: B 581 LEU cc_start: 0.9647 (mp) cc_final: 0.9376 (mt) REVERT: B 604 ASN cc_start: 0.7616 (p0) cc_final: 0.7353 (p0) REVERT: B 629 ASN cc_start: 0.8866 (m110) cc_final: 0.8305 (m-40) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.0791 time to fit residues: 32.7182 Evaluate side-chains 237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 283 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 40 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119111 restraints weight = 17027.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121811 restraints weight = 10725.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123405 restraints weight = 7774.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124817 restraints weight = 6320.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125439 restraints weight = 5458.670| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9092 Z= 0.125 Angle : 0.611 6.824 12324 Z= 0.303 Chirality : 0.041 0.178 1427 Planarity : 0.004 0.070 1522 Dihedral : 5.428 52.717 1255 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.21 % Allowed : 1.24 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.43 (0.21), residues: 604 sheet: -0.68 (0.81), residues: 34 loop : -2.73 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 163 TYR 0.014 0.001 TYR B 464 PHE 0.029 0.002 PHE B 489 TRP 0.008 0.001 TRP B 624 HIS 0.008 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 ( 9089) covalent geometry : angle 0.61049 / 0.30 (12318) SS BOND : bond 0.00539 / 0.24 ( 3) SS BOND : angle 1.14253 / 0.69 ( 6) hydrogen bonds : bond 0.03052 / 2.07 ( 365) hydrogen bonds : angle 4.57742 / 3.19 ( 1059) *********************** 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 283 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7781 (t70) cc_final: 0.7533 (t0) REVERT: A 119 CYS cc_start: 0.7083 (t) cc_final: 0.6768 (t) REVERT: A 120 ASN cc_start: 0.7971 (p0) cc_final: 0.7315 (m-40) REVERT: A 143 SER cc_start: 0.7881 (p) cc_final: 0.7676 (p) REVERT: A 187 SER cc_start: 0.8155 (m) cc_final: 0.7727 (p) REVERT: A 192 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8794 (mmmm) REVERT: A 238 ILE cc_start: 0.9088 (mp) cc_final: 0.8750 (mp) REVERT: A 240 PHE cc_start: 0.8771 (p90) cc_final: 0.8304 (p90) REVERT: A 277 PHE cc_start: 0.6661 (m-80) cc_final: 0.6101 (m-80) REVERT: A 346 LYS cc_start: 0.7642 (tptp) cc_final: 0.7319 (mtpp) REVERT: A 458 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 514 MET cc_start: 0.8080 (ptp) cc_final: 0.7617 (ptt) REVERT: A 557 ASN cc_start: 0.8272 (t0) cc_final: 0.7878 (m-40) REVERT: A 617 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7652 (mm-40) REVERT: B 71 MET cc_start: 0.7632 (mmm) cc_final: 0.6766 (mmm) REVERT: B 96 ARG cc_start: 0.7932 (mmt90) cc_final: 0.7322 (mmm-85) REVERT: B 105 ASP cc_start: 0.7453 (t0) cc_final: 0.7225 (t0) REVERT: B 143 SER cc_start: 0.8311 (p) cc_final: 0.8018 (t) REVERT: B 160 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8010 (tpt-90) REVERT: B 187 SER cc_start: 0.8139 (m) cc_final: 0.7768 (p) REVERT: B 199 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6478 (mm-30) REVERT: B 238 ILE cc_start: 0.9185 (mp) cc_final: 0.8977 (mp) REVERT: B 277 PHE cc_start: 0.6664 (m-80) cc_final: 0.6177 (m-80) REVERT: B 342 TYR cc_start: 0.7359 (t80) cc_final: 0.7075 (t80) REVERT: B 442 VAL cc_start: 0.8671 (t) cc_final: 0.8427 (m) REVERT: B 458 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 604 ASN cc_start: 0.7519 (p0) cc_final: 0.7238 (p0) REVERT: B 629 ASN cc_start: 0.8861 (m110) cc_final: 0.8316 (m-40) outliers start: 2 outliers final: 1 residues processed: 283 average time/residue: 0.0799 time to fit residues: 32.7520 Evaluate side-chains 238 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 158 ASN A 283 HIS A 424 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 40 HIS B 68 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119865 restraints weight = 16969.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122607 restraints weight = 10625.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124499 restraints weight = 7641.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125784 restraints weight = 6123.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126497 restraints weight = 5280.092| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9092 Z= 0.126 Angle : 0.641 9.364 12324 Z= 0.316 Chirality : 0.042 0.203 1427 Planarity : 0.004 0.065 1522 Dihedral : 5.410 52.286 1255 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.21 % Allowed : 1.04 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -2.03 (0.25), residues: 1116 helix: -0.36 (0.21), residues: 604 sheet: -0.61 (0.81), residues: 34 loop : -2.75 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 163 TYR 0.017 0.001 TYR A 494 PHE 0.028 0.002 PHE A 545 TRP 0.008 0.001 TRP B 624 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9089) covalent geometry : angle 0.64116 / 0.32 (12318) SS BOND : bond 0.00362 / 0.16 ( 3) SS BOND : angle 1.00950 / 0.64 ( 6) hydrogen bonds : bond 0.03158 / 2.09 ( 365) hydrogen bonds : angle 4.61971 / 3.22 ( 1059) *********************** 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 273 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7928 (p0) cc_final: 0.7594 (p0) REVERT: A 187 SER cc_start: 0.8195 (m) cc_final: 0.7766 (p) REVERT: A 192 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8729 (mmmm) REVERT: A 238 ILE cc_start: 0.9093 (mp) cc_final: 0.8753 (mp) REVERT: A 240 PHE cc_start: 0.8833 (p90) cc_final: 0.8322 (p90) REVERT: A 277 PHE cc_start: 0.6656 (m-80) cc_final: 0.6090 (m-80) REVERT: A 346 LYS cc_start: 0.7602 (tptp) cc_final: 0.7271 (mtpp) REVERT: A 423 ILE cc_start: 0.9123 (tp) cc_final: 0.8743 (mt) REVERT: A 458 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 514 MET cc_start: 0.8000 (ptp) cc_final: 0.7545 (ptt) REVERT: A 617 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8569 (mm-40) REVERT: B 71 MET cc_start: 0.7648 (mmm) cc_final: 0.6815 (mmm) REVERT: B 96 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7327 (mmm-85) REVERT: B 105 ASP cc_start: 0.7450 (t0) cc_final: 0.7191 (t0) REVERT: B 153 THR cc_start: 0.8817 (p) cc_final: 0.8409 (p) REVERT: B 160 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8001 (tpt-90) REVERT: B 187 SER cc_start: 0.7890 (m) cc_final: 0.7539 (p) REVERT: B 199 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6638 (mm-30) REVERT: B 238 ILE cc_start: 0.9211 (mp) cc_final: 0.9010 (mp) REVERT: B 277 PHE cc_start: 0.6656 (m-80) cc_final: 0.6195 (m-80) REVERT: B 487 ILE cc_start: 0.8760 (pt) cc_final: 0.8301 (pt) REVERT: B 490 THR cc_start: 0.8496 (p) cc_final: 0.7603 (p) REVERT: B 604 ASN cc_start: 0.7501 (p0) cc_final: 0.7195 (p0) REVERT: B 629 ASN cc_start: 0.8825 (m110) cc_final: 0.8327 (m-40) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.0782 time to fit residues: 31.0630 Evaluate side-chains 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 267 HIS A 283 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 40 HIS B 557 ASN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117232 restraints weight = 17119.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119887 restraints weight = 10734.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121764 restraints weight = 7772.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122787 restraints weight = 6239.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123082 restraints weight = 5434.198| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9092 Z= 0.157 Angle : 0.667 8.879 12324 Z= 0.331 Chirality : 0.043 0.194 1427 Planarity : 0.004 0.064 1522 Dihedral : 5.503 52.935 1255 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.21 % Allowed : 0.62 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -2.03 (0.25), residues: 1116 helix: -0.43 (0.21), residues: 614 sheet: -0.65 (0.81), residues: 34 loop : -2.68 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 163 TYR 0.021 0.002 TYR A 494 PHE 0.032 0.002 PHE A 511 TRP 0.010 0.001 TRP B 624 HIS 0.008 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9089) covalent geometry : angle 0.66708 / 0.33 (12318) SS BOND : bond 0.00468 / 0.22 ( 3) SS BOND : angle 1.07379 / 0.64 ( 6) hydrogen bonds : bond 0.03429 / 2.30 ( 365) hydrogen bonds : angle 4.75302 / 3.32 ( 1059) *********************** 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 275 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7950 (p0) cc_final: 0.7590 (p0) REVERT: A 187 SER cc_start: 0.8233 (m) cc_final: 0.7805 (p) REVERT: A 192 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8737 (mmmm) REVERT: A 199 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7134 (mm-30) REVERT: A 238 ILE cc_start: 0.9126 (mp) cc_final: 0.8837 (mp) REVERT: A 240 PHE cc_start: 0.8888 (p90) cc_final: 0.8435 (p90) REVERT: A 277 PHE cc_start: 0.6774 (m-80) cc_final: 0.6117 (m-80) REVERT: A 346 LYS cc_start: 0.7802 (tptp) cc_final: 0.7480 (mtpp) REVERT: A 423 ILE cc_start: 0.9159 (tp) cc_final: 0.8734 (mt) REVERT: A 458 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 514 MET cc_start: 0.8006 (ptp) cc_final: 0.7623 (ptt) REVERT: A 629 ASN cc_start: 0.8886 (m110) cc_final: 0.8276 (m-40) REVERT: B 71 MET cc_start: 0.7725 (mmm) cc_final: 0.6852 (mmm) REVERT: B 105 ASP cc_start: 0.7605 (t0) cc_final: 0.7296 (t0) REVERT: B 160 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8101 (tpt-90) REVERT: B 199 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6714 (mm-30) REVERT: B 238 ILE cc_start: 0.9239 (mp) cc_final: 0.8984 (mp) REVERT: B 514 MET cc_start: 0.8070 (ptp) cc_final: 0.7462 (ptt) REVERT: B 604 ASN cc_start: 0.7596 (p0) cc_final: 0.7270 (p0) outliers start: 2 outliers final: 1 residues processed: 275 average time/residue: 0.0757 time to fit residues: 30.4654 Evaluate side-chains 235 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 283 HIS A 424 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 40 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119299 restraints weight = 16824.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121988 restraints weight = 10574.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123846 restraints weight = 7653.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124852 restraints weight = 6148.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125838 restraints weight = 5354.927| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9092 Z= 0.131 Angle : 0.673 9.682 12324 Z= 0.330 Chirality : 0.042 0.183 1427 Planarity : 0.004 0.066 1522 Dihedral : 5.424 51.970 1255 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.10 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.25), residues: 1116 helix: -0.23 (0.21), residues: 604 sheet: -0.52 (0.81), residues: 34 loop : -2.81 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 163 TYR 0.019 0.002 TYR B 464 PHE 0.032 0.002 PHE B 545 TRP 0.009 0.001 TRP B 624 HIS 0.005 0.001 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9089) covalent geometry : angle 0.67265 / 0.33 (12318) SS BOND : bond 0.00317 / 0.15 ( 3) SS BOND : angle 1.03032 / 0.64 ( 6) hydrogen bonds : bond 0.03375 / 2.26 ( 365) hydrogen bonds : angle 4.60227 / 3.22 ( 1059) ********************** 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 280 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7793 (p0) cc_final: 0.7505 (p0) REVERT: A 134 LEU cc_start: 0.7590 (mp) cc_final: 0.7295 (tp) REVERT: A 187 SER cc_start: 0.8306 (m) cc_final: 0.7856 (p) REVERT: A 192 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8725 (mmmm) REVERT: A 199 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7083 (mm-30) REVERT: A 238 ILE cc_start: 0.9095 (mp) cc_final: 0.8771 (mp) REVERT: A 240 PHE cc_start: 0.8828 (p90) cc_final: 0.8386 (p90) REVERT: A 277 PHE cc_start: 0.6707 (m-80) cc_final: 0.6056 (m-80) REVERT: A 346 LYS cc_start: 0.7752 (tptp) cc_final: 0.7465 (mtpp) REVERT: A 423 ILE cc_start: 0.9141 (tp) cc_final: 0.8742 (mt) REVERT: A 442 VAL cc_start: 0.8117 (t) cc_final: 0.7898 (t) REVERT: A 458 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 514 MET cc_start: 0.7881 (ptp) cc_final: 0.7543 (ptt) REVERT: B 71 MET cc_start: 0.7647 (mmm) cc_final: 0.6787 (mmm) REVERT: B 105 ASP cc_start: 0.7558 (t0) cc_final: 0.7164 (p0) REVERT: B 163 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7701 (mtm110) REVERT: B 199 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6627 (mm-30) REVERT: B 201 ILE cc_start: 0.9145 (mp) cc_final: 0.8921 (mt) REVERT: B 231 MET cc_start: 0.7857 (tpp) cc_final: 0.7594 (tpp) REVERT: B 233 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8273 (mtmt) REVERT: B 238 ILE cc_start: 0.9169 (mp) cc_final: 0.8954 (mp) REVERT: B 253 PHE cc_start: 0.6916 (m-80) cc_final: 0.6495 (m-80) REVERT: B 384 SER cc_start: 0.9284 (t) cc_final: 0.9058 (t) REVERT: B 442 VAL cc_start: 0.8316 (t) cc_final: 0.8093 (t) REVERT: B 510 MET cc_start: 0.7709 (tpp) cc_final: 0.7498 (tpp) REVERT: B 514 MET cc_start: 0.7929 (ptp) cc_final: 0.7465 (ptt) REVERT: B 523 MET cc_start: 0.8813 (ttt) cc_final: 0.8540 (tmm) REVERT: B 604 ASN cc_start: 0.7472 (p0) cc_final: 0.7187 (p0) REVERT: B 629 ASN cc_start: 0.8922 (m110) cc_final: 0.8299 (m-40) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.0777 time to fit residues: 31.6790 Evaluate side-chains 239 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 0.0270 chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS A 283 HIS A 376 GLN A 391 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 40 HIS B 376 GLN B 557 ASN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123260 restraints weight = 17073.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125990 restraints weight = 10465.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127915 restraints weight = 7474.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128950 restraints weight = 5939.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129983 restraints weight = 5144.114| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9092 Z= 0.112 Angle : 0.662 9.274 12324 Z= 0.321 Chirality : 0.041 0.193 1427 Planarity : 0.004 0.064 1522 Dihedral : 5.334 55.812 1255 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.25), residues: 1116 helix: -0.14 (0.21), residues: 610 sheet: -0.32 (0.82), residues: 34 loop : -2.72 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 163 TYR 0.018 0.001 TYR B 463 PHE 0.033 0.002 PHE A 511 TRP 0.010 0.001 TRP A 379 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 9089) covalent geometry : angle 0.66132 / 0.32 (12318) SS BOND : bond 0.00319 / 0.15 ( 3) SS BOND : angle 1.09175 / 0.66 ( 6) hydrogen bonds : bond 0.03176 / 2.10 ( 365) hydrogen bonds : angle 4.46202 / 3.13 ( 1059) =============================================================================== Job complete usr+sys time: 1519.21 seconds wall clock time: 27 minutes 2.65 seconds (1622.65 seconds total)