Starting phenix.real_space_refine on Fri Oct 23 18:49:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25jp_80160/10_2026/25jp_80160.cif Found real_map, /net/cci-nas-00/data/ceres_data/25jp_80160/10_2026/25jp_80160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25jp_80160/10_2026/25jp_80160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25jp_80160/10_2026/25jp_80160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25jp_80160/10_2026/25jp_80160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25jp_80160/10_2026/25jp_80160.map" } resolution = 3.36 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.004 sd= 0.152 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6959 2.51 5 N 1695 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10611 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5270 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5380 Chain: "B" Number of atoms: 5273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5376 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 4.23, per 1000 atoms: 0.40 Number of scatterers: 10611 At special positions: 0 Unit cell: (118.483, 92.395, 108.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 60 16.00 P 4 15.00 O 1891 8.00 N 1695 7.00 C 6959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 728.4 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 62.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.690A pdb=" N PHE A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 removed outlier: 4.735A pdb=" N VAL A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.930A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.705A pdb=" N GLU A 154 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.795A pdb=" N PHE A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 4.159A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.934A pdb=" N VAL A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.727A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 309 removed outlier: 3.754A pdb=" N THR A 309 " --> pdb=" O LEU A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 315 through 319 removed outlier: 4.262A pdb=" N GLY A 319 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 349 removed outlier: 3.939A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 364 through 367 Proline residue: A 367 - end of helix No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 368 through 402 removed outlier: 3.750A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 441 removed outlier: 4.246A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.130A pdb=" N ILE A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 4.097A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 537 removed outlier: 4.044A pdb=" N MET A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.827A pdb=" N ILE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 582 removed outlier: 4.355A pdb=" N SER A 575 " --> pdb=" O THR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 654 removed outlier: 3.900A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.718A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.552A pdb=" N LYS A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.652A pdb=" N PHE A 757 " --> pdb=" O HIS A 753 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 768 Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.697A pdb=" N PHE B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 4.739A pdb=" N VAL B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.930A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.871A pdb=" N GLU B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.633A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 4.164A pdb=" N LYS B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 4.166A pdb=" N SER B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.967A pdb=" N VAL B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 269 Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.714A pdb=" N LYS B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.763A pdb=" N THR B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 removed outlier: 3.643A pdb=" N ASP B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 349 removed outlier: 3.940A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Proline residue: B 336 - end of helix Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 364 through 367 Proline residue: B 367 - end of helix No H-bonds generated for 'chain 'B' and resid 364 through 367' Processing helix chain 'B' and resid 368 through 402 removed outlier: 3.749A pdb=" N THR B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 374 " --> pdb=" O TRP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 441 removed outlier: 4.239A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 472 removed outlier: 4.014A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 500 removed outlier: 4.101A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 537 removed outlier: 4.027A pdb=" N MET B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.806A pdb=" N ILE B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 removed outlier: 4.371A pdb=" N SER B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 654 removed outlier: 3.896A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 727 removed outlier: 3.756A pdb=" N LYS B 726 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.558A pdb=" N LYS B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.660A pdb=" N PHE B 757 " --> pdb=" O HIS B 753 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 611 removed outlier: 6.241A pdb=" N ASN A 554 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N HIS A 585 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL A 556 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL A 587 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY A 558 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL A 589 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY A 560 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 591 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE A 562 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 593 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY A 733 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N LEU A 777 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR A 783 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 785 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR A 738 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AA4, first strand: chain 'B' and resid 608 through 611 removed outlier: 6.289A pdb=" N ASN B 554 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N HIS B 585 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL B 556 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL B 587 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 558 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 589 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY B 560 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 591 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE B 562 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE B 593 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY B 733 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LEU B 777 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR B 730 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 779 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET B 732 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET B 781 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU B 734 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR B 783 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B 736 " --> pdb=" O TYR B 783 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 785 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR B 738 " --> pdb=" O LEU B 785 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1475 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: 1.45 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1888 1.33 - 1.45: 2786 1.45 - 1.57: 6066 1.57 - 1.69: 6 1.69 - 1.81: 104 Bond restraints: 10850 Sorted by residual: bond pdb=" CA ALA A 313 " pdb=" CB ALA A 313 " ideal model delta sigma weight residual 1.537 1.470 0.066 1.41e-02 5.03e+03 2.22e+01 bond pdb=" N ILE A 199 " pdb=" CA ILE A 199 " ideal model delta sigma weight residual 1.457 1.497 -0.040 9.30e-03 1.16e+04 1.85e+01 bond pdb=" CA SER B 300 " pdb=" CB SER B 300 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.54e-02 4.22e+03 1.65e+01 bond pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.53e+01 bond pdb=" CA TYR A 139 " pdb=" C TYR A 139 " ideal model delta sigma weight residual 1.525 1.479 0.047 1.27e-02 6.20e+03 1.34e+01 ... (remaining 10845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 14469 2.85 - 5.69: 237 5.69 - 8.54: 23 8.54 - 11.38: 7 11.38 - 14.23: 3 Bond angle restraints: 14739 Sorted by residual: angle pdb=" N ILE A 199 " pdb=" CA ILE A 199 " pdb=" C ILE A 199 " ideal model delta sigma weight residual 113.20 100.08 13.12 9.60e-01 1.09e+00 1.87e+02 angle pdb=" N ALA A 313 " pdb=" CA ALA A 313 " pdb=" C ALA A 313 " ideal model delta sigma weight residual 114.12 99.89 14.23 1.39e+00 5.18e-01 1.05e+02 angle pdb=" N ALA B 231 " pdb=" CA ALA B 231 " pdb=" C ALA B 231 " ideal model delta sigma weight residual 114.75 104.23 10.52 1.26e+00 6.30e-01 6.97e+01 angle pdb=" N ILE B 299 " pdb=" CA ILE B 299 " pdb=" C ILE B 299 " ideal model delta sigma weight residual 112.90 105.10 7.80 9.60e-01 1.09e+00 6.60e+01 angle pdb=" N ALA A 231 " pdb=" CA ALA A 231 " pdb=" C ALA A 231 " ideal model delta sigma weight residual 114.75 104.54 10.21 1.26e+00 6.30e-01 6.57e+01 ... (remaining 14734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 5773 21.81 - 43.61: 486 43.61 - 65.42: 81 65.42 - 87.23: 8 87.23 - 109.04: 3 Dihedral angle restraints: 6351 sinusoidal: 2466 harmonic: 3885 Sorted by residual: dihedral pdb=" CA LEU B 438 " pdb=" C LEU B 438 " pdb=" N ALA B 439 " pdb=" CA ALA B 439 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 49.03 -109.04 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" CA ILE B 512 " pdb=" C ILE B 512 " pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 6348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1504 0.068 - 0.136: 204 0.136 - 0.203: 13 0.203 - 0.271: 4 0.271 - 0.339: 3 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB VAL B 457 " pdb=" CA VAL B 457 " pdb=" CG1 VAL B 457 " pdb=" CG2 VAL B 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 457 " pdb=" CA VAL A 457 " pdb=" CG1 VAL A 457 " pdb=" CG2 VAL A 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1725 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 472 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ILE A 472 " -0.075 2.00e-02 2.50e+03 pdb=" O ILE A 472 " 0.028 2.00e-02 2.50e+03 pdb=" N TRP A 473 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 138 " -0.377 9.50e-02 1.11e+02 1.69e-01 1.75e+01 pdb=" NE ARG A 138 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 138 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 138 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 138 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 458 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C MET B 458 " 0.067 2.00e-02 2.50e+03 pdb=" O MET B 458 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL B 459 " -0.023 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.74: 1455 2.74 - 3.34: 11581 3.34 - 3.94: 18553 3.94 - 4.54: 26489 4.54 - 5.14: 42679 Nonbonded interactions: 100757 Sorted by model distance: nonbonded pdb=" O TYR A 563 " pdb=" O2' ADP A 901 " model vdw 2.145 3.040 nonbonded pdb=" OE1 GLU A 565 " pdb=" O HOH A1001 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR B 107 " pdb=" OH TYR B 335 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR A 107 " pdb=" OH TYR A 335 " model vdw 2.184 3.040 nonbonded pdb=" O HOH B1005 " pdb=" O HOH B1006 " model vdw 2.196 3.040 ... (remaining 100752 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 55 through 138 or resid 140 through 529 or resid 531 throu \ gh 902)) selection = (chain 'B' and (resid 55 through 138 or resid 140 through 529 or resid 531 throu \ gh 902)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.450 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.006 0.066 10850 Z= 0.291 Angle : 0.894 14.228 14739 Z= 0.563 Chirality : 0.049 0.339 1728 Planarity : 0.007 0.169 1787 Dihedral : 16.096 109.037 3867 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.36 % Favored : 91.19 % Rotamer: Outliers : 3.97 % Allowed : 17.27 % Favored : 78.76 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.20), residues: 1318 helix: -2.52 (0.15), residues: 782 sheet: -2.31 (0.51), residues: 102 loop : -2.93 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.013 0.002 TYR A 139 PHE 0.010 0.001 PHE B 268 TRP 0.012 0.001 TRP A 258 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.29 (10850) covalent geometry : angle 0.89438 / 0.56 (14739) hydrogen bonds : bond 0.16669 / 11.10 ( 522) hydrogen bonds : angle 7.09209 / 4.76 ( 1475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.342 Fit side-chains REVERT: A 141 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7362 (mttm) REVERT: A 151 GLU cc_start: 0.7169 (pm20) cc_final: 0.6685 (tm-30) REVERT: A 158 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7817 (t80) REVERT: A 474 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.5611 (mtmt) REVERT: A 499 MET cc_start: 0.7169 (tpt) cc_final: 0.6674 (ttp) REVERT: A 570 ILE cc_start: 0.8617 (mp) cc_final: 0.8391 (mt) REVERT: A 724 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6987 (ttt90) REVERT: B 158 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 416 TYR cc_start: 0.7826 (m-80) cc_final: 0.7624 (m-80) REVERT: B 441 ARG cc_start: 0.8465 (ptp90) cc_final: 0.8243 (ptm-80) REVERT: B 474 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6085 (tttt) REVERT: B 499 MET cc_start: 0.7188 (tpt) cc_final: 0.6742 (ttp) REVERT: B 760 LYS cc_start: 0.7469 (tttp) cc_final: 0.5938 (mmmt) outliers start: 45 outliers final: 30 residues processed: 250 average time/residue: 0.1156 time to fit residues: 39.7678 Evaluate side-chains 215 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 598 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 355 ASN A 385 GLN A 419 GLN A 448 HIS A 527 HIS A 716 GLN B 64 GLN B 355 ASN B 385 GLN B 419 GLN B 527 HIS B 716 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143187 restraints weight = 16428.797| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.33 r_work: 0.3401 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10850 Z= 0.197 Angle : 0.693 9.138 14739 Z= 0.364 Chirality : 0.045 0.198 1728 Planarity : 0.005 0.048 1787 Dihedral : 9.232 112.968 1532 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.32 % Allowed : 18.48 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1318 helix: -1.27 (0.18), residues: 784 sheet: -2.05 (0.52), residues: 102 loop : -2.26 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 640 TYR 0.019 0.002 TYR A 644 PHE 0.015 0.001 PHE A 268 TRP 0.012 0.001 TRP A 258 HIS 0.005 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (10850) covalent geometry : angle 0.69254 / 0.36 (14739) hydrogen bonds : bond 0.05822 / 3.77 ( 522) hydrogen bonds : angle 4.67384 / 3.14 ( 1475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.343 Fit side-chains REVERT: A 120 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7392 (mp-120) REVERT: A 158 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7852 (t80) REVERT: A 288 TYR cc_start: 0.7893 (m-10) cc_final: 0.7660 (m-10) REVERT: A 458 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: A 499 MET cc_start: 0.7720 (tpt) cc_final: 0.6300 (tmm) REVERT: A 570 ILE cc_start: 0.8669 (mp) cc_final: 0.8448 (mt) REVERT: A 724 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7447 (ttt90) REVERT: B 158 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 288 TYR cc_start: 0.7876 (m-10) cc_final: 0.7635 (m-10) REVERT: B 416 TYR cc_start: 0.7744 (m-80) cc_final: 0.7522 (m-80) REVERT: B 474 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5829 (mtmt) REVERT: B 499 MET cc_start: 0.7567 (tpt) cc_final: 0.6196 (tmm) REVERT: B 760 LYS cc_start: 0.7802 (tttp) cc_final: 0.5988 (mmmt) outliers start: 49 outliers final: 33 residues processed: 217 average time/residue: 0.1101 time to fit residues: 33.0013 Evaluate side-chains 214 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [92, 56, 67, 4, 19, 126, 68, 55, 7, 91, 96] chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.174634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146337 restraints weight = 16354.429| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.34 r_work: 0.3471 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10850 Z= 0.147 Angle : 0.630 8.437 14739 Z= 0.328 Chirality : 0.043 0.171 1728 Planarity : 0.005 0.046 1787 Dihedral : 8.383 112.642 1505 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.54 % Allowed : 20.38 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1318 helix: -0.57 (0.19), residues: 784 sheet: -1.88 (0.52), residues: 102 loop : -1.87 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 640 TYR 0.023 0.001 TYR B 644 PHE 0.014 0.001 PHE B 268 TRP 0.010 0.001 TRP A 258 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10850) covalent geometry : angle 0.63027 / 0.33 (14739) hydrogen bonds : bond 0.04846 / 3.16 ( 522) hydrogen bonds : angle 4.20102 / 2.82 ( 1475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.394 Fit side-chains REVERT: A 59 MET cc_start: 0.7968 (mmt) cc_final: 0.7705 (mmt) REVERT: A 116 PHE cc_start: 0.8985 (m-10) cc_final: 0.8601 (m-10) REVERT: A 120 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: A 158 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7788 (t80) REVERT: A 288 TYR cc_start: 0.7843 (m-10) cc_final: 0.7498 (m-10) REVERT: A 469 MET cc_start: 0.8162 (ttm) cc_final: 0.7401 (ttp) REVERT: A 499 MET cc_start: 0.7658 (tpt) cc_final: 0.6209 (tmm) REVERT: A 570 ILE cc_start: 0.8604 (mp) cc_final: 0.8388 (mt) REVERT: A 724 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7354 (ttt90) REVERT: B 158 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7755 (t80) REVERT: B 288 TYR cc_start: 0.7826 (m-10) cc_final: 0.7477 (m-10) REVERT: B 416 TYR cc_start: 0.7591 (m-80) cc_final: 0.7363 (m-80) REVERT: B 474 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5778 (mtmt) REVERT: B 499 MET cc_start: 0.7534 (tpt) cc_final: 0.6155 (tmm) REVERT: B 760 LYS cc_start: 0.7733 (tttp) cc_final: 0.5924 (mmmt) outliers start: 40 outliers final: 31 residues processed: 209 average time/residue: 0.1027 time to fit residues: 30.3851 Evaluate side-chains 213 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [39, 22, 93, 84, 35, 64, 53, 86, 99, 49, 107] chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.0170 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 86 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151554 restraints weight = 16699.852| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.38 r_work: 0.3534 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10850 Z= 0.107 Angle : 0.576 7.485 14739 Z= 0.297 Chirality : 0.042 0.168 1728 Planarity : 0.004 0.048 1787 Dihedral : 7.975 112.646 1504 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.85 % Allowed : 22.28 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.24), residues: 1318 helix: -0.20 (0.20), residues: 784 sheet: -1.71 (0.52), residues: 102 loop : -1.54 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 724 TYR 0.018 0.001 TYR B 644 PHE 0.014 0.001 PHE A 182 TRP 0.008 0.001 TRP B 523 HIS 0.003 0.000 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10850) covalent geometry : angle 0.57612 / 0.30 (14739) hydrogen bonds : bond 0.03734 / 2.47 ( 522) hydrogen bonds : angle 3.85478 / 2.59 ( 1475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.287 Fit side-chains REVERT: A 59 MET cc_start: 0.8034 (mmt) cc_final: 0.7787 (mmt) REVERT: A 116 PHE cc_start: 0.8936 (m-10) cc_final: 0.8481 (m-10) REVERT: A 120 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: A 151 GLU cc_start: 0.7202 (pm20) cc_final: 0.6467 (tm-30) REVERT: A 469 MET cc_start: 0.8148 (ttm) cc_final: 0.7306 (ttp) REVERT: A 499 MET cc_start: 0.7652 (tpt) cc_final: 0.6179 (tmm) REVERT: A 592 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7961 (t) REVERT: A 724 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7467 (ttt90) REVERT: B 141 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7094 (mttm) REVERT: B 416 TYR cc_start: 0.7513 (m-80) cc_final: 0.7290 (m-80) REVERT: B 444 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: B 474 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5589 (mtmt) REVERT: B 499 MET cc_start: 0.7610 (tpt) cc_final: 0.6202 (tmm) REVERT: B 760 LYS cc_start: 0.7540 (tttp) cc_final: 0.5836 (mmmt) outliers start: 32 outliers final: 20 residues processed: 208 average time/residue: 0.0964 time to fit residues: 28.7816 Evaluate side-chains 189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [20, 104, 128, 26, 125, 44, 35, 93, 22, 40, 57] chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 128 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151213 restraints weight = 21522.999| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.11 r_work: 0.3505 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10850 Z= 0.112 Angle : 0.588 7.638 14739 Z= 0.301 Chirality : 0.041 0.149 1728 Planarity : 0.004 0.049 1787 Dihedral : 7.767 110.475 1498 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.45 % Allowed : 22.54 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.93 (0.24), residues: 1318 helix: 0.06 (0.20), residues: 782 sheet: -1.58 (0.52), residues: 102 loop : -1.44 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 724 TYR 0.013 0.001 TYR B 644 PHE 0.013 0.001 PHE B 268 TRP 0.010 0.001 TRP B 298 HIS 0.002 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10850) covalent geometry : angle 0.58843 / 0.30 (14739) hydrogen bonds : bond 0.03775 / 2.49 ( 522) hydrogen bonds : angle 3.77876 / 2.54 ( 1475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.369 Fit side-chains REVERT: A 59 MET cc_start: 0.8029 (mmt) cc_final: 0.7788 (mmt) REVERT: A 116 PHE cc_start: 0.8942 (m-10) cc_final: 0.8715 (m-10) REVERT: A 151 GLU cc_start: 0.7108 (pm20) cc_final: 0.6390 (tm-30) REVERT: A 172 MET cc_start: 0.7332 (tpp) cc_final: 0.6909 (tpp) REVERT: A 287 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6661 (mm) REVERT: A 469 MET cc_start: 0.7956 (ttm) cc_final: 0.7662 (ttm) REVERT: A 499 MET cc_start: 0.7688 (tpt) cc_final: 0.6065 (tmm) REVERT: A 592 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8002 (t) REVERT: A 724 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7469 (ttt90) REVERT: B 141 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7141 (mttm) REVERT: B 287 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6702 (mm) REVERT: B 416 TYR cc_start: 0.7441 (m-80) cc_final: 0.7224 (m-80) REVERT: B 444 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: B 474 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5590 (mttm) REVERT: B 499 MET cc_start: 0.7639 (tpt) cc_final: 0.6194 (tmm) REVERT: B 760 LYS cc_start: 0.7546 (tttp) cc_final: 0.5766 (mmmt) outliers start: 39 outliers final: 25 residues processed: 195 average time/residue: 0.0991 time to fit residues: 27.7220 Evaluate side-chains 192 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [119, 32, 26, 49, 43, 124, 131, 34, 74, 130, 94] chunk 119 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151645 restraints weight = 18783.983| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.71 r_work: 0.3533 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10850 Z= 0.111 Angle : 0.574 6.893 14739 Z= 0.293 Chirality : 0.041 0.147 1728 Planarity : 0.004 0.050 1787 Dihedral : 7.594 109.706 1498 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.02 % Allowed : 23.06 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1318 helix: 0.14 (0.20), residues: 800 sheet: -1.47 (0.52), residues: 102 loop : -1.21 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 724 TYR 0.012 0.001 TYR B 644 PHE 0.013 0.001 PHE A 182 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10850) covalent geometry : angle 0.57443 / 0.29 (14739) hydrogen bonds : bond 0.03746 / 2.46 ( 522) hydrogen bonds : angle 3.73514 / 2.51 ( 1475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.389 Fit side-chains REVERT: A 59 MET cc_start: 0.8069 (mmt) cc_final: 0.7825 (mmt) REVERT: A 151 GLU cc_start: 0.7038 (pm20) cc_final: 0.6332 (tm-30) REVERT: A 287 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6671 (mm) REVERT: A 469 MET cc_start: 0.7866 (ttm) cc_final: 0.7586 (ttm) REVERT: A 499 MET cc_start: 0.7683 (tpt) cc_final: 0.6095 (tmm) REVERT: A 546 GLN cc_start: 0.8219 (tp40) cc_final: 0.7940 (tt0) REVERT: A 592 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8162 (t) REVERT: A 724 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7456 (ttt90) REVERT: B 141 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7139 (mttm) REVERT: B 287 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6774 (mm) REVERT: B 416 TYR cc_start: 0.7470 (m-80) cc_final: 0.7256 (m-80) REVERT: B 444 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: B 458 MET cc_start: 0.8062 (mmm) cc_final: 0.7584 (mmt) REVERT: B 469 MET cc_start: 0.8142 (ttp) cc_final: 0.7934 (ttp) REVERT: B 474 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5531 (mttm) REVERT: B 499 MET cc_start: 0.7638 (tpt) cc_final: 0.6131 (tmm) REVERT: B 519 MET cc_start: 0.8340 (tmm) cc_final: 0.8121 (ttt) REVERT: B 546 GLN cc_start: 0.8204 (tp40) cc_final: 0.7971 (tt0) REVERT: B 760 LYS cc_start: 0.7473 (tttp) cc_final: 0.5745 (mmmt) outliers start: 34 outliers final: 28 residues processed: 198 average time/residue: 0.0957 time to fit residues: 27.4063 Evaluate side-chains 202 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [27, 112, 16, 71, 128, 74, 43, 86, 50, 29, 80] chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148861 restraints weight = 17578.601| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.49 r_work: 0.3479 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10850 Z= 0.141 Angle : 0.602 8.519 14739 Z= 0.308 Chirality : 0.042 0.149 1728 Planarity : 0.004 0.050 1787 Dihedral : 7.636 110.850 1497 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.80 % Allowed : 22.71 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1318 helix: 0.18 (0.20), residues: 796 sheet: -1.43 (0.52), residues: 102 loop : -1.19 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 724 TYR 0.009 0.001 TYR B 628 PHE 0.010 0.001 PHE B 268 TRP 0.009 0.001 TRP B 258 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (10850) covalent geometry : angle 0.60208 / 0.31 (14739) hydrogen bonds : bond 0.04318 / 2.81 ( 522) hydrogen bonds : angle 3.82543 / 2.57 ( 1475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.365 Fit side-chains REVERT: A 151 GLU cc_start: 0.7035 (pm20) cc_final: 0.6363 (tm-30) REVERT: A 287 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6718 (mm) REVERT: A 469 MET cc_start: 0.8047 (ttm) cc_final: 0.7786 (ttm) REVERT: A 499 MET cc_start: 0.7690 (tpt) cc_final: 0.6212 (tmm) REVERT: A 546 GLN cc_start: 0.8243 (tp40) cc_final: 0.7954 (tt0) REVERT: A 592 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8058 (t) REVERT: A 724 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7398 (ttt90) REVERT: B 287 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6805 (mm) REVERT: B 444 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: B 458 MET cc_start: 0.8095 (mmm) cc_final: 0.7606 (mmt) REVERT: B 469 MET cc_start: 0.8212 (ttp) cc_final: 0.7987 (ttp) REVERT: B 474 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5479 (mttm) REVERT: B 499 MET cc_start: 0.7588 (tpt) cc_final: 0.6119 (tmm) REVERT: B 546 GLN cc_start: 0.8219 (tp40) cc_final: 0.7950 (tt0) REVERT: B 760 LYS cc_start: 0.7585 (tttp) cc_final: 0.5803 (mmmt) outliers start: 43 outliers final: 32 residues processed: 202 average time/residue: 0.0987 time to fit residues: 28.7832 Evaluate side-chains 204 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [17, 47, 100, 63, 7, 43, 5, 38, 19, 72, 95] chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149956 restraints weight = 20941.298| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.02 r_work: 0.3505 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10850 Z= 0.123 Angle : 0.588 7.733 14739 Z= 0.300 Chirality : 0.042 0.204 1728 Planarity : 0.004 0.052 1787 Dihedral : 7.546 110.051 1497 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.54 % Allowed : 23.32 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1318 helix: 0.31 (0.20), residues: 794 sheet: -1.38 (0.52), residues: 102 loop : -1.15 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 724 TYR 0.009 0.001 TYR B 644 PHE 0.014 0.001 PHE A 182 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (10850) covalent geometry : angle 0.58822 / 0.30 (14739) hydrogen bonds : bond 0.04049 / 2.65 ( 522) hydrogen bonds : angle 3.79924 / 2.55 ( 1475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.363 Fit side-chains REVERT: A 151 GLU cc_start: 0.6971 (pm20) cc_final: 0.6283 (tm-30) REVERT: A 287 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6778 (mm) REVERT: A 469 MET cc_start: 0.7882 (ttm) cc_final: 0.7615 (ttm) REVERT: A 499 MET cc_start: 0.7681 (tpt) cc_final: 0.6110 (tmm) REVERT: A 546 GLN cc_start: 0.8231 (tp40) cc_final: 0.7968 (tt0) REVERT: A 592 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8188 (t) REVERT: A 724 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7425 (ttt90) REVERT: B 141 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7080 (mttm) REVERT: B 287 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6820 (mm) REVERT: B 444 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: B 458 MET cc_start: 0.8042 (mmm) cc_final: 0.7521 (mmt) REVERT: B 469 MET cc_start: 0.8135 (ttp) cc_final: 0.7880 (ttp) REVERT: B 474 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5431 (mttm) REVERT: B 499 MET cc_start: 0.7635 (tpt) cc_final: 0.6127 (tmm) REVERT: B 546 GLN cc_start: 0.8206 (tp40) cc_final: 0.7963 (tt0) REVERT: B 760 LYS cc_start: 0.7488 (tttp) cc_final: 0.5734 (mmmt) outliers start: 40 outliers final: 31 residues processed: 195 average time/residue: 0.0914 time to fit residues: 25.6860 Evaluate side-chains 198 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [51, 114, 92, 118, 19, 88, 94, 6, 25, 96, 52] chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150255 restraints weight = 16371.064| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.34 r_work: 0.3513 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10850 Z= 0.124 Angle : 0.587 7.332 14739 Z= 0.300 Chirality : 0.042 0.172 1728 Planarity : 0.004 0.051 1787 Dihedral : 7.448 109.440 1496 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.45 % Allowed : 23.49 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1318 helix: 0.38 (0.20), residues: 794 sheet: -1.33 (0.53), residues: 102 loop : -1.11 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 640 TYR 0.009 0.001 TYR B 644 PHE 0.011 0.001 PHE A 268 TRP 0.009 0.001 TRP A 258 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10850) covalent geometry : angle 0.58680 / 0.30 (14739) hydrogen bonds : bond 0.04055 / 2.64 ( 522) hydrogen bonds : angle 3.80543 / 2.56 ( 1475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.387 Fit side-chains REVERT: A 151 GLU cc_start: 0.6915 (pm20) cc_final: 0.6244 (tm-30) REVERT: A 287 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6814 (mm) REVERT: A 469 MET cc_start: 0.7911 (ttm) cc_final: 0.7706 (ttm) REVERT: A 499 MET cc_start: 0.7721 (tpt) cc_final: 0.6242 (tmm) REVERT: A 546 GLN cc_start: 0.8247 (tp40) cc_final: 0.7992 (tt0) REVERT: A 592 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8175 (t) REVERT: A 724 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7467 (ttt90) REVERT: B 141 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7104 (mttm) REVERT: B 287 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6832 (mm) REVERT: B 444 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 458 MET cc_start: 0.8000 (mmm) cc_final: 0.7665 (mmt) REVERT: B 474 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5477 (mttm) REVERT: B 499 MET cc_start: 0.7659 (tpt) cc_final: 0.6146 (tmm) REVERT: B 546 GLN cc_start: 0.8225 (tp40) cc_final: 0.7984 (tt0) REVERT: B 760 LYS cc_start: 0.7538 (tttp) cc_final: 0.5841 (mmmt) outliers start: 39 outliers final: 32 residues processed: 191 average time/residue: 0.0937 time to fit residues: 25.8960 Evaluate side-chains 198 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [105, 90, 112, 4, 41, 87, 114, 104, 79, 59, 15] chunk 105 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 112 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 87 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 0.0000 chunk 15 optimal weight: 1.9990 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153590 restraints weight = 24635.793| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.41 r_work: 0.3539 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10850 Z= 0.101 Angle : 0.565 9.153 14739 Z= 0.288 Chirality : 0.041 0.169 1728 Planarity : 0.004 0.052 1787 Dihedral : 7.188 107.138 1496 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.50 % Allowed : 24.70 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1318 helix: 0.64 (0.20), residues: 776 sheet: -1.17 (0.54), residues: 102 loop : -1.26 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 640 TYR 0.011 0.001 TYR B 644 PHE 0.011 0.001 PHE A 182 TRP 0.009 0.001 TRP B 298 HIS 0.001 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10850) covalent geometry : angle 0.56513 / 0.29 (14739) hydrogen bonds : bond 0.03357 / 2.22 ( 522) hydrogen bonds : angle 3.68200 / 2.47 ( 1475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.381 Fit side-chains REVERT: A 59 MET cc_start: 0.8034 (mmt) cc_final: 0.7791 (mmt) REVERT: A 116 PHE cc_start: 0.8862 (m-10) cc_final: 0.8647 (m-10) REVERT: A 151 GLU cc_start: 0.6720 (pm20) cc_final: 0.5998 (tm-30) REVERT: A 287 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6710 (mm) REVERT: A 469 MET cc_start: 0.7933 (ttm) cc_final: 0.7170 (ttp) REVERT: A 499 MET cc_start: 0.7697 (tpt) cc_final: 0.6064 (tmm) REVERT: A 546 GLN cc_start: 0.8158 (tp40) cc_final: 0.7928 (tt0) REVERT: A 592 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8177 (t) REVERT: A 640 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7604 (ptp90) REVERT: A 724 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7487 (ttt90) REVERT: B 141 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7091 (mttm) REVERT: B 287 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6776 (mm) REVERT: B 362 ASP cc_start: 0.8028 (m-30) cc_final: 0.7728 (m-30) REVERT: B 416 TYR cc_start: 0.7276 (m-80) cc_final: 0.7066 (m-80) REVERT: B 444 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: B 458 MET cc_start: 0.7909 (mmm) cc_final: 0.7378 (mmt) REVERT: B 474 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5196 (mttm) REVERT: B 499 MET cc_start: 0.7642 (tpt) cc_final: 0.6057 (tmm) REVERT: B 519 MET cc_start: 0.8346 (tmm) cc_final: 0.8127 (ttt) REVERT: B 546 GLN cc_start: 0.8162 (tp40) cc_final: 0.7951 (tt0) REVERT: B 760 LYS cc_start: 0.7488 (tttp) cc_final: 0.5721 (mmmt) outliers start: 28 outliers final: 19 residues processed: 198 average time/residue: 0.0984 time to fit residues: 28.0951 Evaluate side-chains 189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 652 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [0, 35, 113, 107, 75, 9, 65, 61, 63, 117, 11] chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 0.0040 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156543 restraints weight = 12530.713| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.05 r_work: 0.3577 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10850 Z= 0.099 Angle : 0.560 9.230 14739 Z= 0.284 Chirality : 0.040 0.154 1728 Planarity : 0.004 0.048 1787 Dihedral : 6.975 104.690 1496 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.81 % Allowed : 25.82 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1318 helix: 0.81 (0.20), residues: 772 sheet: -0.96 (0.55), residues: 102 loop : -1.21 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 640 TYR 0.011 0.001 TYR B 644 PHE 0.011 0.001 PHE A 182 TRP 0.010 0.001 TRP B 479 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (10850) covalent geometry : angle 0.56022 / 0.28 (14739) hydrogen bonds : bond 0.03161 / 2.08 ( 522) hydrogen bonds : angle 3.64755 / 2.45 ( 1475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.66 seconds wall clock time: 41 minutes 56.81 seconds (2516.81 seconds total)