Starting phenix.real_space_refine on Tue Sep 24 23:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/09_2024/6vxj_21440.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/09_2024/6vxj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/09_2024/6vxj_21440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/09_2024/6vxj_21440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/09_2024/6vxj_21440.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/09_2024/6vxj_21440.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 6.02, per 1000 atoms: 0.68 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 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: 0.91 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: 2.40 Time building geometry restraints manager: 2.93 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: 4745 16.99 - 33.98: 536 33.98 - 50.97: 160 50.97 - 67.96: 48 67.96 - 84.95: 12 Dihedral angle restraints: 5501 sinusoidal: 2241 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 5498 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 9089 Z= 0.454 Angle : 1.017 9.420 12318 Z= 0.548 Chirality : 0.055 0.289 1427 Planarity : 0.006 0.084 1522 Dihedral : 16.515 83.686 3400 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP B 627 HIS 0.003 0.001 HIS B 375 PHE 0.019 0.002 PHE A 489 TYR 0.012 0.002 TYR A 613 ARG 0.002 0.001 ARG B 137 *********************** 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 fitting. rotamer outliers: 32 poor density : 325 time to evaluate : 1.114 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: 0.8829 (t80) cc_final: 0.8620 (t80) REVERT: A 514 MET cc_start: 0.8620 (ptp) cc_final: 0.8208 (ptt) REVERT: A 518 TYR cc_start: 0.9095 (m-10) cc_final: 0.8891 (m-80) REVERT: A 533 VAL cc_start: 0.8837 (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: 0.7210 (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: 0.7926 (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: 0.8374 (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: 0.8824 (tp30) cc_final: 0.8493 (mm-30) REVERT: B 605 TYR cc_start: 0.5857 (m-80) cc_final: 0.5301 (m-80) REVERT: B 629 ASN cc_start: 0.8956 (m-40) cc_final: 0.8474 (m-40) REVERT: B 630 HIS cc_start: 0.8543 (m170) cc_final: 0.8249 (m170) REVERT: B 636 MET cc_start: 0.8253 (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: 0.2225 time to fit residues: 101.0848 Evaluate side-chains 249 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 68 ASN A 76 ASN A 109 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS A 601 ASN A 629 ASN A 630 HIS B 40 HIS B 76 ASN B 109 ASN B 141 GLN 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9089 Z= 0.193 Angle : 0.645 7.072 12318 Z= 0.328 Chirality : 0.041 0.174 1427 Planarity : 0.005 0.078 1522 Dihedral : 7.005 54.308 1382 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.31 % Allowed : 4.36 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.21), residues: 1116 helix: -2.24 (0.17), residues: 632 sheet: -1.11 (0.74), residues: 34 loop : -3.18 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 379 HIS 0.009 0.001 HIS A 283 PHE 0.019 0.002 PHE B 489 TYR 0.012 0.001 TYR A 459 ARG 0.003 0.000 ARG A 482 *********************** 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 317 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 314 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8386 (tttt) cc_final: 0.8009 (ttpt) REVERT: A 137 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7768 (ttm110) REVERT: A 143 SER cc_start: 0.7685 (p) cc_final: 0.7439 (p) REVERT: A 192 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8526 (mmmm) REVERT: A 240 PHE cc_start: 0.8623 (p90) cc_final: 0.7951 (p90) REVERT: A 266 PHE cc_start: 0.8107 (t80) cc_final: 0.7753 (t80) REVERT: A 336 TYR cc_start: 0.7971 (t80) cc_final: 0.7687 (t80) REVERT: A 470 PHE cc_start: 0.8724 (t80) cc_final: 0.8180 (t80) REVERT: A 514 MET cc_start: 0.8633 (ptp) cc_final: 0.8176 (ptt) REVERT: A 548 MET cc_start: 0.7868 (mtt) cc_final: 0.7235 (mtt) REVERT: A 557 ASN cc_start: 0.8123 (t0) cc_final: 0.7390 (m-40) REVERT: A 565 LEU cc_start: 0.9097 (tp) cc_final: 0.8867 (tp) REVERT: A 573 ILE cc_start: 0.9207 (mt) cc_final: 0.8935 (mt) REVERT: A 617 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8029 (mm-40) REVERT: A 629 ASN cc_start: 0.9052 (m110) cc_final: 0.8687 (m-40) REVERT: A 652 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8501 (tttt) REVERT: B 71 MET cc_start: 0.7840 (mmm) cc_final: 0.7200 (mmm) REVERT: B 96 ARG cc_start: 0.8187 (ttt180) cc_final: 0.7842 (mmm-85) REVERT: B 105 ASP cc_start: 0.7890 (t70) cc_final: 0.7678 (t0) REVERT: B 160 ARG cc_start: 0.8475 (ttm110) cc_final: 0.7724 (tpt170) REVERT: B 198 MET cc_start: 0.9120 (ttm) cc_final: 0.8624 (ttm) REVERT: B 253 PHE cc_start: 0.7478 (m-80) cc_final: 0.7155 (m-80) REVERT: B 458 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7563 (tp30) REVERT: B 477 ASP cc_start: 0.8134 (t0) cc_final: 0.7915 (t0) REVERT: B 514 MET cc_start: 0.8675 (ptp) cc_final: 0.8073 (ptt) REVERT: B 523 MET cc_start: 0.8665 (tpt) cc_final: 0.8364 (tpt) REVERT: B 585 GLU cc_start: 0.8602 (tp30) cc_final: 0.8375 (mm-30) outliers start: 3 outliers final: 0 residues processed: 316 average time/residue: 0.1958 time to fit residues: 86.7795 Evaluate side-chains 243 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 283 HIS A 398 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9089 Z= 0.401 Angle : 0.756 10.665 12318 Z= 0.385 Chirality : 0.044 0.187 1427 Planarity : 0.005 0.070 1522 Dihedral : 7.568 51.306 1382 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1116 helix: -1.28 (0.19), residues: 598 sheet: -1.16 (0.81), residues: 34 loop : -3.08 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.008 0.002 HIS B 630 PHE 0.027 0.003 PHE B 506 TYR 0.018 0.002 TYR A 494 ARG 0.007 0.001 ARG B 163 *********************** 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 293 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7989 (mmt) cc_final: 0.7496 (mmm) REVERT: A 81 PRO cc_start: 0.8469 (Cg_endo) cc_final: 0.7908 (Cg_exo) REVERT: A 86 LYS cc_start: 0.8595 (tttt) cc_final: 0.8240 (ttpt) REVERT: A 143 SER cc_start: 0.8009 (p) cc_final: 0.7803 (p) REVERT: A 192 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8518 (mmmm) REVERT: A 240 PHE cc_start: 0.8870 (p90) cc_final: 0.8430 (p90) REVERT: A 266 PHE cc_start: 0.8337 (t80) cc_final: 0.8081 (t80) REVERT: A 276 TYR cc_start: 0.7841 (t80) cc_final: 0.7159 (t80) REVERT: A 336 TYR cc_start: 0.8372 (t80) cc_final: 0.8167 (t80) REVERT: A 458 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 477 ASP cc_start: 0.8060 (t0) cc_final: 0.7860 (t0) REVERT: A 557 ASN cc_start: 0.8260 (t0) cc_final: 0.7884 (m-40) REVERT: A 617 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8209 (mm-40) REVERT: A 629 ASN cc_start: 0.9061 (m110) cc_final: 0.8426 (m-40) REVERT: A 652 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8494 (tttt) REVERT: B 71 MET cc_start: 0.7896 (mmm) cc_final: 0.6923 (mmm) REVERT: B 160 ARG cc_start: 0.8830 (ttm110) cc_final: 0.7761 (tpt-90) REVERT: B 346 LYS cc_start: 0.7703 (tptp) cc_final: 0.7470 (mtpp) REVERT: B 424 GLN cc_start: 0.6711 (tt0) cc_final: 0.6456 (mt0) REVERT: B 458 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 460 ILE cc_start: 0.9079 (tp) cc_final: 0.8796 (tp) REVERT: B 470 PHE cc_start: 0.8992 (t80) cc_final: 0.8742 (t80) REVERT: B 646 LEU cc_start: 0.8649 (tt) cc_final: 0.8199 (mm) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.1832 time to fit residues: 75.4994 Evaluate side-chains 236 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 0.0050 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 283 HIS A 398 GLN A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9089 Z= 0.203 Angle : 0.614 9.807 12318 Z= 0.306 Chirality : 0.040 0.139 1427 Planarity : 0.004 0.063 1522 Dihedral : 6.655 49.000 1382 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.23), residues: 1116 helix: -0.89 (0.20), residues: 604 sheet: -0.94 (0.78), residues: 34 loop : -2.93 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 624 HIS 0.003 0.001 HIS B 630 PHE 0.024 0.002 PHE A 545 TYR 0.016 0.001 TYR A 464 ARG 0.005 0.001 ARG B 193 *********************** 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 295 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PRO cc_start: 0.8376 (Cg_endo) cc_final: 0.7920 (Cg_exo) REVERT: A 86 LYS cc_start: 0.8553 (tttt) cc_final: 0.8331 (ttpt) REVERT: A 141 GLN cc_start: 0.8270 (mp-120) cc_final: 0.7778 (mp10) REVERT: A 143 SER cc_start: 0.7956 (p) cc_final: 0.7749 (p) REVERT: A 192 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8645 (mmmm) REVERT: A 240 PHE cc_start: 0.8722 (p90) cc_final: 0.8268 (p90) REVERT: A 346 LYS cc_start: 0.7695 (tptp) cc_final: 0.7362 (mtpp) REVERT: A 430 LEU cc_start: 0.9447 (mt) cc_final: 0.9237 (mt) REVERT: A 458 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 510 MET cc_start: 0.8280 (ttm) cc_final: 0.8076 (ttm) REVERT: A 514 MET cc_start: 0.8053 (ptp) cc_final: 0.7781 (ptt) REVERT: A 548 MET cc_start: 0.8080 (mtt) cc_final: 0.7705 (mtt) REVERT: A 557 ASN cc_start: 0.8319 (t0) cc_final: 0.7886 (m-40) REVERT: A 617 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8055 (mm-40) REVERT: A 652 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8476 (tttt) REVERT: B 71 MET cc_start: 0.7784 (mmm) cc_final: 0.7049 (mmm) REVERT: B 143 SER cc_start: 0.8466 (p) cc_final: 0.8257 (p) REVERT: B 160 ARG cc_start: 0.8786 (ttm110) cc_final: 0.7916 (tpt-90) REVERT: B 163 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7528 (mtm110) REVERT: B 238 ILE cc_start: 0.9321 (mp) cc_final: 0.9096 (mp) REVERT: B 277 PHE cc_start: 0.6450 (m-80) cc_final: 0.5997 (m-80) REVERT: B 346 LYS cc_start: 0.7751 (tptp) cc_final: 0.7428 (mtpp) REVERT: B 424 GLN cc_start: 0.6763 (tt0) cc_final: 0.6547 (mt0) REVERT: B 430 LEU cc_start: 0.9472 (mt) cc_final: 0.9258 (mt) REVERT: B 460 ILE cc_start: 0.9027 (tp) cc_final: 0.8706 (tp) REVERT: B 470 PHE cc_start: 0.8978 (t80) cc_final: 0.8651 (t80) REVERT: B 514 MET cc_start: 0.7816 (ptp) cc_final: 0.7596 (ptt) REVERT: B 604 ASN cc_start: 0.7570 (p0) cc_final: 0.7321 (p0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1791 time to fit residues: 74.7649 Evaluate side-chains 242 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 283 HIS A 391 ASN A 393 GLN A 398 GLN A 630 HIS B 222 ASN B 267 HIS B 391 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9089 Z= 0.432 Angle : 0.782 7.656 12318 Z= 0.397 Chirality : 0.046 0.176 1427 Planarity : 0.005 0.066 1522 Dihedral : 7.596 54.805 1382 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1116 helix: -1.01 (0.20), residues: 614 sheet: -0.84 (0.83), residues: 34 loop : -2.86 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.007 0.002 HIS A 267 PHE 0.044 0.003 PHE A 489 TYR 0.030 0.003 TYR A 494 ARG 0.004 0.001 ARG B 163 *********************** 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 275 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8085 (Cg_exo) REVERT: A 141 GLN cc_start: 0.8375 (mp-120) cc_final: 0.7836 (mp10) REVERT: A 192 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8944 (mmmt) REVERT: A 240 PHE cc_start: 0.8928 (p90) cc_final: 0.8494 (p90) REVERT: A 276 TYR cc_start: 0.7527 (t80) cc_final: 0.6843 (t80) REVERT: A 346 LYS cc_start: 0.7757 (tptp) cc_final: 0.7376 (mtpp) REVERT: A 430 LEU cc_start: 0.9388 (mt) cc_final: 0.9125 (mt) REVERT: A 458 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 514 MET cc_start: 0.8350 (ptp) cc_final: 0.7879 (ptt) REVERT: A 557 ASN cc_start: 0.8322 (t0) cc_final: 0.7810 (m-40) REVERT: A 617 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8102 (mm-40) REVERT: A 629 ASN cc_start: 0.8873 (m110) cc_final: 0.8331 (m-40) REVERT: A 652 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8455 (tttt) REVERT: B 71 MET cc_start: 0.7933 (mmm) cc_final: 0.6891 (mmm) REVERT: B 105 ASP cc_start: 0.7879 (t0) cc_final: 0.7583 (t0) REVERT: B 160 ARG cc_start: 0.8837 (ttm110) cc_final: 0.7996 (tpt-90) REVERT: B 199 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7021 (mm-30) REVERT: B 346 LYS cc_start: 0.7974 (tptp) cc_final: 0.7657 (mtpp) REVERT: B 424 GLN cc_start: 0.6764 (tt0) cc_final: 0.6426 (mt0) REVERT: B 430 LEU cc_start: 0.9531 (mt) cc_final: 0.9327 (mt) REVERT: B 460 ILE cc_start: 0.9053 (tp) cc_final: 0.8792 (tp) REVERT: B 470 PHE cc_start: 0.8872 (t80) cc_final: 0.8508 (t80) REVERT: B 478 LEU cc_start: 0.8507 (tt) cc_final: 0.8251 (tt) REVERT: B 514 MET cc_start: 0.8128 (ptp) cc_final: 0.7730 (ptt) REVERT: B 629 ASN cc_start: 0.8994 (m110) cc_final: 0.8332 (m-40) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1818 time to fit residues: 70.6126 Evaluate side-chains 227 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 overall best weight: 2.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9089 Z= 0.268 Angle : 0.666 6.473 12318 Z= 0.332 Chirality : 0.042 0.168 1427 Planarity : 0.005 0.062 1522 Dihedral : 7.164 57.549 1382 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1116 helix: -0.70 (0.20), residues: 606 sheet: -0.84 (0.82), residues: 34 loop : -2.87 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 624 HIS 0.005 0.001 HIS B 630 PHE 0.034 0.002 PHE A 489 TYR 0.017 0.002 TYR B 494 ARG 0.007 0.001 ARG B 163 *********************** 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 277 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7990 (tttp) cc_final: 0.7748 (ttmm) REVERT: A 141 GLN cc_start: 0.8422 (mp-120) cc_final: 0.7940 (mp10) REVERT: A 192 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8840 (mmmm) REVERT: A 199 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 240 PHE cc_start: 0.8842 (p90) cc_final: 0.8377 (p90) REVERT: A 266 PHE cc_start: 0.8359 (t80) cc_final: 0.7921 (t80) REVERT: A 276 TYR cc_start: 0.7756 (t80) cc_final: 0.6678 (t80) REVERT: A 277 PHE cc_start: 0.6549 (m-80) cc_final: 0.6152 (m-80) REVERT: A 346 LYS cc_start: 0.7802 (tptp) cc_final: 0.7481 (mtpp) REVERT: A 458 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 514 MET cc_start: 0.8356 (ptp) cc_final: 0.7812 (ptt) REVERT: A 557 ASN cc_start: 0.8334 (t0) cc_final: 0.7746 (m-40) REVERT: A 617 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8092 (mm-40) REVERT: A 629 ASN cc_start: 0.8884 (m110) cc_final: 0.8334 (m-40) REVERT: A 652 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8365 (tttt) REVERT: B 71 MET cc_start: 0.7818 (mmm) cc_final: 0.6911 (mmm) REVERT: B 105 ASP cc_start: 0.7817 (t0) cc_final: 0.7542 (t0) REVERT: B 131 MET cc_start: 0.8224 (mmm) cc_final: 0.7866 (mmm) REVERT: B 152 MET cc_start: 0.6407 (ptp) cc_final: 0.6144 (ptp) REVERT: B 160 ARG cc_start: 0.8783 (ttm110) cc_final: 0.7979 (tpt-90) REVERT: B 199 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7081 (mm-30) REVERT: B 346 LYS cc_start: 0.7982 (tptp) cc_final: 0.7650 (mtpp) REVERT: B 424 GLN cc_start: 0.6609 (tt0) cc_final: 0.6314 (mt0) REVERT: B 430 LEU cc_start: 0.9527 (mt) cc_final: 0.9294 (mt) REVERT: B 460 ILE cc_start: 0.9061 (tp) cc_final: 0.8732 (tp) REVERT: B 478 LEU cc_start: 0.8447 (tt) cc_final: 0.8173 (tt) REVERT: B 514 MET cc_start: 0.7972 (ptp) cc_final: 0.7648 (ptt) REVERT: B 604 ASN cc_start: 0.7746 (p0) cc_final: 0.7460 (p0) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1798 time to fit residues: 70.7968 Evaluate side-chains 232 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 283 HIS A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9089 Z= 0.197 Angle : 0.644 8.394 12318 Z= 0.316 Chirality : 0.042 0.303 1427 Planarity : 0.004 0.060 1522 Dihedral : 6.667 59.593 1382 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.24), residues: 1116 helix: -0.64 (0.20), residues: 610 sheet: -0.53 (0.84), residues: 34 loop : -2.80 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.006 0.001 HIS A 267 PHE 0.022 0.002 PHE A 489 TYR 0.015 0.001 TYR B 494 ARG 0.008 0.000 ARG B 163 *********************** 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 280 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7974 (tttp) cc_final: 0.7749 (ttmm) REVERT: A 119 CYS cc_start: 0.7350 (t) cc_final: 0.6997 (t) REVERT: A 120 ASN cc_start: 0.8075 (p0) cc_final: 0.7393 (m-40) REVERT: A 141 GLN cc_start: 0.8257 (mp-120) cc_final: 0.7907 (mp10) REVERT: A 153 THR cc_start: 0.8926 (p) cc_final: 0.8615 (p) REVERT: A 187 SER cc_start: 0.8339 (m) cc_final: 0.7898 (p) REVERT: A 192 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8798 (mmmm) REVERT: A 199 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 240 PHE cc_start: 0.8764 (p90) cc_final: 0.8313 (p90) REVERT: A 276 TYR cc_start: 0.7689 (t80) cc_final: 0.6682 (t80) REVERT: A 277 PHE cc_start: 0.6477 (m-80) cc_final: 0.6140 (m-80) REVERT: A 346 LYS cc_start: 0.7863 (tptp) cc_final: 0.7582 (mtpp) REVERT: A 442 VAL cc_start: 0.8480 (t) cc_final: 0.8273 (t) REVERT: A 458 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 514 MET cc_start: 0.8349 (ptp) cc_final: 0.7774 (ptt) REVERT: A 523 MET cc_start: 0.8984 (ttm) cc_final: 0.8765 (tmm) REVERT: A 557 ASN cc_start: 0.8337 (t0) cc_final: 0.7759 (m-40) REVERT: A 617 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8063 (mm-40) REVERT: A 652 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8285 (ttpt) REVERT: B 71 MET cc_start: 0.7695 (mmm) cc_final: 0.6824 (mmm) REVERT: B 105 ASP cc_start: 0.7701 (t0) cc_final: 0.7212 (p0) REVERT: B 131 MET cc_start: 0.8226 (mmm) cc_final: 0.7950 (mmm) REVERT: B 160 ARG cc_start: 0.8772 (ttm110) cc_final: 0.7970 (tpt-90) REVERT: B 199 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7001 (mm-30) REVERT: B 346 LYS cc_start: 0.7936 (tptp) cc_final: 0.7666 (mtpp) REVERT: B 424 GLN cc_start: 0.6478 (tt0) cc_final: 0.6244 (mt0) REVERT: B 430 LEU cc_start: 0.9457 (mt) cc_final: 0.9212 (mt) REVERT: B 478 LEU cc_start: 0.8440 (tt) cc_final: 0.8171 (tt) REVERT: B 523 MET cc_start: 0.8954 (ttm) cc_final: 0.8708 (tmm) REVERT: B 604 ASN cc_start: 0.7612 (p0) cc_final: 0.7374 (p0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1790 time to fit residues: 71.6784 Evaluate side-chains 235 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 630 HIS B 41 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9089 Z= 0.309 Angle : 0.710 7.864 12318 Z= 0.352 Chirality : 0.044 0.232 1427 Planarity : 0.005 0.063 1522 Dihedral : 6.949 59.351 1382 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1116 helix: -0.53 (0.20), residues: 608 sheet: -0.53 (0.83), residues: 34 loop : -2.86 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.003 0.001 HIS A 155 PHE 0.038 0.002 PHE B 489 TYR 0.020 0.002 TYR B 464 ARG 0.008 0.001 ARG B 163 *********************** 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 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7437 (t) cc_final: 0.7018 (t) REVERT: A 120 ASN cc_start: 0.8163 (p0) cc_final: 0.7456 (m-40) REVERT: A 131 MET cc_start: 0.7724 (mmm) cc_final: 0.7214 (mmm) REVERT: A 187 SER cc_start: 0.8200 (m) cc_final: 0.7829 (p) REVERT: A 192 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8804 (mmmm) REVERT: A 199 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 240 PHE cc_start: 0.8903 (p90) cc_final: 0.8480 (p90) REVERT: A 276 TYR cc_start: 0.7765 (t80) cc_final: 0.7172 (t80) REVERT: A 277 PHE cc_start: 0.6547 (m-80) cc_final: 0.6130 (m-80) REVERT: A 346 LYS cc_start: 0.7840 (tptp) cc_final: 0.7518 (mtpp) REVERT: A 458 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 514 MET cc_start: 0.8520 (ptp) cc_final: 0.7892 (ptt) REVERT: A 523 MET cc_start: 0.8927 (ttm) cc_final: 0.8721 (tmm) REVERT: A 557 ASN cc_start: 0.8334 (t0) cc_final: 0.7736 (m-40) REVERT: A 617 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8057 (mm-40) REVERT: A 652 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8338 (tttt) REVERT: B 71 MET cc_start: 0.7718 (mmm) cc_final: 0.6822 (mmm) REVERT: B 105 ASP cc_start: 0.7865 (t0) cc_final: 0.7544 (t0) REVERT: B 131 MET cc_start: 0.8275 (mmm) cc_final: 0.7988 (mmm) REVERT: B 160 ARG cc_start: 0.8745 (ttm110) cc_final: 0.7930 (tpt-90) REVERT: B 199 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 276 TYR cc_start: 0.7847 (t80) cc_final: 0.7176 (t80) REVERT: B 346 LYS cc_start: 0.7977 (tptp) cc_final: 0.7688 (mtpp) REVERT: B 424 GLN cc_start: 0.6592 (tt0) cc_final: 0.6268 (mt0) REVERT: B 478 LEU cc_start: 0.8438 (tt) cc_final: 0.8213 (tt) REVERT: B 523 MET cc_start: 0.8968 (ttm) cc_final: 0.8665 (tmm) REVERT: B 604 ASN cc_start: 0.7776 (p0) cc_final: 0.7513 (p0) REVERT: B 629 ASN cc_start: 0.8912 (m110) cc_final: 0.8290 (m-40) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1895 time to fit residues: 71.7517 Evaluate side-chains 228 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 283 HIS A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9089 Z= 0.204 Angle : 0.670 9.359 12318 Z= 0.326 Chirality : 0.042 0.165 1427 Planarity : 0.004 0.059 1522 Dihedral : 6.582 59.785 1382 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.25), residues: 1116 helix: -0.44 (0.21), residues: 618 sheet: -0.56 (0.81), residues: 34 loop : -2.83 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 624 HIS 0.007 0.001 HIS A 267 PHE 0.038 0.002 PHE B 489 TYR 0.014 0.001 TYR A 464 ARG 0.009 0.000 ARG B 163 *********************** 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 272 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7990 (p0) cc_final: 0.7624 (p0) REVERT: A 131 MET cc_start: 0.7808 (mmm) cc_final: 0.7369 (mmm) REVERT: A 141 GLN cc_start: 0.8347 (mp-120) cc_final: 0.7894 (mp10) REVERT: A 187 SER cc_start: 0.8359 (m) cc_final: 0.7897 (p) REVERT: A 192 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8795 (mmmm) REVERT: A 238 ILE cc_start: 0.9198 (mp) cc_final: 0.8911 (mp) REVERT: A 240 PHE cc_start: 0.8834 (p90) cc_final: 0.8391 (p90) REVERT: A 276 TYR cc_start: 0.7782 (t80) cc_final: 0.7069 (t80) REVERT: A 277 PHE cc_start: 0.6524 (m-80) cc_final: 0.6177 (m-80) REVERT: A 346 LYS cc_start: 0.7793 (tptp) cc_final: 0.7419 (ttpp) REVERT: A 442 VAL cc_start: 0.8162 (t) cc_final: 0.7958 (t) REVERT: A 458 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 514 MET cc_start: 0.8422 (ptp) cc_final: 0.7778 (ptt) REVERT: A 604 ASN cc_start: 0.8108 (p0) cc_final: 0.7616 (p0) REVERT: A 652 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8297 (tttt) REVERT: B 71 MET cc_start: 0.7654 (mmm) cc_final: 0.6784 (mmm) REVERT: B 105 ASP cc_start: 0.7705 (t0) cc_final: 0.7279 (p0) REVERT: B 131 MET cc_start: 0.8265 (mmm) cc_final: 0.8010 (mmm) REVERT: B 143 SER cc_start: 0.8598 (p) cc_final: 0.8364 (t) REVERT: B 160 ARG cc_start: 0.8824 (ttm110) cc_final: 0.7991 (tpt-90) REVERT: B 199 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 233 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8286 (mtmt) REVERT: B 238 ILE cc_start: 0.9233 (mp) cc_final: 0.8996 (mp) REVERT: B 253 PHE cc_start: 0.6950 (m-80) cc_final: 0.6490 (m-80) REVERT: B 346 LYS cc_start: 0.7924 (tptp) cc_final: 0.7661 (mtpp) REVERT: B 478 LEU cc_start: 0.8385 (tt) cc_final: 0.8153 (tt) REVERT: B 487 ILE cc_start: 0.8859 (pt) cc_final: 0.8312 (pt) REVERT: B 490 THR cc_start: 0.8520 (p) cc_final: 0.8265 (p) REVERT: B 511 PHE cc_start: 0.8609 (t80) cc_final: 0.8051 (t80) REVERT: B 523 MET cc_start: 0.8908 (ttm) cc_final: 0.8581 (tmm) REVERT: B 604 ASN cc_start: 0.7636 (p0) cc_final: 0.7395 (p0) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1843 time to fit residues: 71.9689 Evaluate side-chains 232 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 376 GLN A 557 ASN A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9089 Z= 0.178 Angle : 0.674 10.576 12318 Z= 0.325 Chirality : 0.041 0.162 1427 Planarity : 0.004 0.062 1522 Dihedral : 6.080 50.005 1382 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.25), residues: 1116 helix: -0.28 (0.21), residues: 606 sheet: -0.90 (0.71), residues: 44 loop : -2.81 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 624 HIS 0.003 0.000 HIS B 630 PHE 0.036 0.002 PHE B 489 TYR 0.017 0.001 TYR A 459 ARG 0.009 0.000 ARG B 163 ********************** 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 287 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7309 (t) cc_final: 0.6940 (t) REVERT: A 120 ASN cc_start: 0.7875 (p0) cc_final: 0.7283 (m-40) REVERT: A 131 MET cc_start: 0.7806 (mmm) cc_final: 0.7414 (mmm) REVERT: A 134 LEU cc_start: 0.7499 (mp) cc_final: 0.7240 (tp) REVERT: A 141 GLN cc_start: 0.8205 (mp-120) cc_final: 0.7852 (mp10) REVERT: A 187 SER cc_start: 0.8399 (m) cc_final: 0.7957 (p) REVERT: A 192 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8791 (mmmm) REVERT: A 238 ILE cc_start: 0.9094 (mp) cc_final: 0.8891 (mp) REVERT: A 253 PHE cc_start: 0.7164 (m-80) cc_final: 0.6796 (m-80) REVERT: A 276 TYR cc_start: 0.7517 (t80) cc_final: 0.6713 (t80) REVERT: A 277 PHE cc_start: 0.6581 (m-80) cc_final: 0.6057 (m-80) REVERT: A 346 LYS cc_start: 0.7815 (tptp) cc_final: 0.7541 (mtpp) REVERT: A 384 SER cc_start: 0.9299 (t) cc_final: 0.9051 (t) REVERT: A 458 GLU cc_start: 0.8158 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 463 TYR cc_start: 0.7996 (m-80) cc_final: 0.7229 (m-80) REVERT: A 514 MET cc_start: 0.8292 (ptp) cc_final: 0.7738 (ptt) REVERT: A 652 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8132 (ttpt) REVERT: B 71 MET cc_start: 0.7524 (mmm) cc_final: 0.6788 (mmm) REVERT: B 105 ASP cc_start: 0.7644 (t0) cc_final: 0.7289 (p0) REVERT: B 106 VAL cc_start: 0.8588 (t) cc_final: 0.8375 (t) REVERT: B 131 MET cc_start: 0.8162 (mmm) cc_final: 0.7958 (mmm) REVERT: B 143 SER cc_start: 0.8552 (p) cc_final: 0.8278 (t) REVERT: B 160 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8029 (tpt-90) REVERT: B 163 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7494 (mtm110) REVERT: B 199 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6639 (mm-30) REVERT: B 233 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8311 (mtmt) REVERT: B 238 ILE cc_start: 0.9173 (mp) cc_final: 0.8944 (mp) REVERT: B 346 LYS cc_start: 0.7898 (tptp) cc_final: 0.7688 (mtpp) REVERT: B 419 ASP cc_start: 0.8845 (p0) cc_final: 0.8026 (p0) REVERT: B 478 LEU cc_start: 0.8323 (tt) cc_final: 0.8092 (tt) REVERT: B 510 MET cc_start: 0.7926 (tpp) cc_final: 0.7705 (tpp) REVERT: B 511 PHE cc_start: 0.8594 (t80) cc_final: 0.8251 (t80) REVERT: B 523 MET cc_start: 0.8837 (ttm) cc_final: 0.8534 (tmm) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2058 time to fit residues: 84.5871 Evaluate side-chains 248 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 376 GLN A 630 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112956 restraints weight = 17186.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115585 restraints weight = 10593.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117406 restraints weight = 7574.340| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9089 Z= 0.380 Angle : 0.760 7.871 12318 Z= 0.381 Chirality : 0.047 0.247 1427 Planarity : 0.005 0.063 1522 Dihedral : 6.860 55.924 1382 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.25), residues: 1116 helix: -0.41 (0.21), residues: 606 sheet: -0.84 (0.77), residues: 44 loop : -2.84 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 624 HIS 0.007 0.001 HIS A 267 PHE 0.028 0.003 PHE B 489 TYR 0.024 0.002 TYR B 494 ARG 0.010 0.001 ARG B 163 =============================================================================== Job complete usr+sys time: 2114.61 seconds wall clock time: 38 minutes 28.42 seconds (2308.42 seconds total)