Starting phenix.real_space_refine on Wed Mar 4 14:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dge_30672/03_2026/7dge_30672_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dge_30672/03_2026/7dge_30672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dge_30672/03_2026/7dge_30672_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dge_30672/03_2026/7dge_30672_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dge_30672/03_2026/7dge_30672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dge_30672/03_2026/7dge_30672.map" } resolution = 3.65 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9110 2.51 5 N 2403 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14249 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6183 Classifications: {'peptide': 784} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 751} Chain breaks: 1 Chain: "B" Number of atoms: 6183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6183 Classifications: {'peptide': 784} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 751} Chain breaks: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.48, per 1000 atoms: 0.24 Number of scatterers: 14249 At special positions: 0 Unit cell: (169.52, 144.56, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2628 8.00 N 2403 7.00 C 9110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.01 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 543 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 394 " distance=2.00 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 439 " distance=1.99 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 544 " distance=2.02 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 547 " distance=2.02 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 562 " distance=2.04 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 578 " distance=2.00 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.01 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 543 " distance=2.01 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 439 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 544 " distance=2.02 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 547 " distance=2.02 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 562 " distance=2.02 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 578 " distance=2.04 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 412.6 milliseconds 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3368 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 18 sheets defined 43.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.574A pdb=" N GLN A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.559A pdb=" N ASP A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.606A pdb=" N GLN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.642A pdb=" N PHE A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.553A pdb=" N LEU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.860A pdb=" N ASN A 335 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.715A pdb=" N ASP A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 409 through 432 removed outlier: 3.773A pdb=" N CYS A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 573 through 576 Processing helix chain 'A' and resid 590 through 615 removed outlier: 5.247A pdb=" N ALA A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 649 removed outlier: 4.017A pdb=" N CYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Proline residue: A 645 - end of helix removed outlier: 3.766A pdb=" N ILE A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 702 through 728 removed outlier: 4.759A pdb=" N GLN A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 775 removed outlier: 3.728A pdb=" N ALA A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Proline residue: A 756 - end of helix removed outlier: 5.110A pdb=" N LYS A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 774 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 806 Proline residue: A 803 - end of helix Processing helix chain 'A' and resid 811 through 831 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'B' and resid 75 through 90 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.109A pdb=" N ASP B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 4.350A pdb=" N GLN B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.627A pdb=" N LEU B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.999A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'B' and resid 292 through 307 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.504A pdb=" N ALA B 321 " --> pdb=" O ASP B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.687A pdb=" N ASP B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 376 Processing helix chain 'B' and resid 409 through 432 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 508 through 516 removed outlier: 5.267A pdb=" N GLN B 513 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N MET B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 515 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 576 removed outlier: 4.187A pdb=" N THR B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 618 removed outlier: 4.250A pdb=" N ALA B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 617 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 644 removed outlier: 3.621A pdb=" N CYS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 689 removed outlier: 3.506A pdb=" N LEU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY B 665 " --> pdb=" O ARG B 661 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 675 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 727 removed outlier: 4.361A pdb=" N ALA B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 771 Proline residue: B 756 - end of helix Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing helix chain 'B' and resid 782 through 807 removed outlier: 4.095A pdb=" N ILE B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) Proline residue: B 803 - end of helix Processing helix chain 'B' and resid 811 through 831 Processing helix chain 'B' and resid 831 through 838 removed outlier: 3.615A pdb=" N MET B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.634A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 64 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.660A pdb=" N ILE A 47 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG A 106 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 49 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 46 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 159 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 48 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.249A pdb=" N GLN A 182 " --> pdb=" O LEU A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 232 removed outlier: 8.455A pdb=" N VAL A 227 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ASP A 259 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA A 229 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 261 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N HIS A 231 " --> pdb=" O ILE A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 342 removed outlier: 4.115A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 483 " --> pdb=" O HIS A 496 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN A 485 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR A 494 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 460 Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 535 removed outlier: 3.643A pdb=" N THR A 548 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 558 removed outlier: 3.796A pdb=" N GLN A 557 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 569 through 571 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.472A pdb=" N VAL B 45 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 104 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 47 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG B 106 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 49 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 159 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 182 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 258 through 261 removed outlier: 7.225A pdb=" N ALA B 229 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 261 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS B 231 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 338 through 342 removed outlier: 6.777A pdb=" N TYR B 479 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR B 499 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE B 481 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB4, first strand: chain 'B' and resid 569 through 570 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.652A pdb=" N GLN C 5 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 14 through 15 removed outlier: 6.634A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 60 through 62 removed outlier: 5.315A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 114 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 9 Processing sheet with id=AB9, first strand: chain 'D' and resid 60 through 62 removed outlier: 5.304A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2332 1.32 - 1.45: 4135 1.45 - 1.57: 7948 1.57 - 1.70: 0 1.70 - 1.83: 154 Bond restraints: 14569 Sorted by residual: bond pdb=" CD GLU A 370 " pdb=" OE1 GLU A 370 " ideal model delta sigma weight residual 1.249 1.357 -0.108 1.90e-02 2.77e+03 3.24e+01 bond pdb=" CG ASP A 208 " pdb=" OD2 ASP A 208 " ideal model delta sigma weight residual 1.249 1.357 -0.108 1.90e-02 2.77e+03 3.24e+01 bond pdb=" CD GLU A 386 " pdb=" OE1 GLU A 386 " ideal model delta sigma weight residual 1.249 1.355 -0.106 1.90e-02 2.77e+03 3.09e+01 bond pdb=" CD GLU B 238 " pdb=" OE2 GLU B 238 " ideal model delta sigma weight residual 1.249 1.353 -0.104 1.90e-02 2.77e+03 3.01e+01 bond pdb=" CA PRO A 57 " pdb=" C PRO A 57 " ideal model delta sigma weight residual 1.514 1.544 -0.030 5.50e-03 3.31e+04 2.93e+01 ... (remaining 14564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 17068 2.82 - 5.65: 2481 5.65 - 8.47: 191 8.47 - 11.30: 10 11.30 - 14.12: 3 Bond angle restraints: 19753 Sorted by residual: angle pdb=" C PHE B 368 " pdb=" N GLN B 369 " pdb=" CA GLN B 369 " ideal model delta sigma weight residual 120.54 130.51 -9.97 1.35e+00 5.49e-01 5.46e+01 angle pdb=" C ALA B 636 " pdb=" N GLY B 637 " pdb=" CA GLY B 637 " ideal model delta sigma weight residual 119.99 127.82 -7.83 1.13e+00 7.83e-01 4.80e+01 angle pdb=" CA CYS B 657 " pdb=" CB CYS B 657 " pdb=" SG CYS B 657 " ideal model delta sigma weight residual 114.40 100.28 14.12 2.30e+00 1.89e-01 3.77e+01 angle pdb=" C ASP D 64 " pdb=" N SER D 65 " pdb=" CA SER D 65 " ideal model delta sigma weight residual 120.38 129.03 -8.65 1.46e+00 4.69e-01 3.51e+01 angle pdb=" C LEU A 757 " pdb=" N GLY A 758 " pdb=" CA GLY A 758 " ideal model delta sigma weight residual 120.00 126.46 -6.46 1.10e+00 8.26e-01 3.45e+01 ... (remaining 19748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7691 17.88 - 35.76: 868 35.76 - 53.64: 141 53.64 - 71.53: 19 71.53 - 89.41: 7 Dihedral angle restraints: 8726 sinusoidal: 3466 harmonic: 5260 Sorted by residual: dihedral pdb=" CB CYS A 657 " pdb=" SG CYS A 657 " pdb=" SG CYS A 746 " pdb=" CB CYS A 746 " ideal model delta sinusoidal sigma weight residual -86.00 -164.55 78.55 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS B 565 " pdb=" SG CYS B 565 " pdb=" SG CYS B 578 " pdb=" CB CYS B 578 " ideal model delta sinusoidal sigma weight residual 93.00 157.88 -64.88 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA HIS B 496 " pdb=" C HIS B 496 " pdb=" N VAL B 497 " pdb=" CA VAL B 497 " ideal model delta harmonic sigma weight residual 180.00 143.24 36.76 0 5.00e+00 4.00e-02 5.41e+01 ... (remaining 8723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1612 0.131 - 0.262: 523 0.262 - 0.392: 64 0.392 - 0.523: 9 0.523 - 0.654: 1 Chirality restraints: 2209 Sorted by residual: chirality pdb=" CB THR B 679 " pdb=" CA THR B 679 " pdb=" OG1 THR B 679 " pdb=" CG2 THR B 679 " both_signs ideal model delta sigma weight residual False 2.55 1.90 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB THR A 793 " pdb=" CA THR A 793 " pdb=" OG1 THR A 793 " pdb=" CG2 THR A 793 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB VAL B 610 " pdb=" CA VAL B 610 " pdb=" CG1 VAL B 610 " pdb=" CG2 VAL B 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 2206 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 330 " -0.179 2.00e-02 2.50e+03 1.04e-01 2.18e+02 pdb=" CG TYR B 330 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 330 " 0.104 2.00e-02 2.50e+03 pdb=" CD2 TYR B 330 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR B 330 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 330 " 0.088 2.00e-02 2.50e+03 pdb=" CZ TYR B 330 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 330 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 672 " -0.181 2.00e-02 2.50e+03 9.52e-02 1.81e+02 pdb=" CG TYR A 672 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 672 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 672 " 0.108 2.00e-02 2.50e+03 pdb=" CE1 TYR A 672 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 672 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 672 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 672 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 672 " -0.173 2.00e-02 2.50e+03 9.10e-02 1.66e+02 pdb=" CG TYR B 672 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B 672 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR B 672 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR B 672 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 672 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR B 672 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 672 " -0.127 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6554 2.98 - 3.46: 15990 3.46 - 3.94: 24056 3.94 - 4.42: 27862 4.42 - 4.90: 43517 Nonbonded interactions: 117979 Sorted by model distance: nonbonded pdb=" OE2 GLU B 386 " pdb=" O SER D 59 " model vdw 2.503 3.040 nonbonded pdb=" O PHE A 801 " pdb=" N TYR A 805 " model vdw 2.511 3.120 nonbonded pdb=" OG1 THR D 93 " pdb=" O VAL D 121 " model vdw 2.512 3.040 nonbonded pdb=" N HIS B 501 " pdb=" O HIS B 501 " model vdw 2.531 2.496 nonbonded pdb=" N THR B 653 " pdb=" O THR B 653 " model vdw 2.542 2.496 ... (remaining 117974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 839) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.013 0.108 14588 Z= 0.751 Angle : 1.987 14.124 19791 Z= 1.326 Chirality : 0.122 0.654 2209 Planarity : 0.015 0.160 2502 Dihedral : 14.951 89.407 5301 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.15 % Favored : 87.01 % Rotamer: Outliers : 2.25 % Allowed : 10.28 % Favored : 87.47 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.12 % 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: -4.67 (0.16), residues: 1802 helix: -2.83 (0.14), residues: 689 sheet: -3.15 (0.30), residues: 218 loop : -3.31 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 280 TYR 0.181 0.024 TYR A 672 PHE 0.105 0.022 PHE D 39 TRP 0.131 0.024 TRP B 798 HIS 0.024 0.006 HIS B 428 Details of bonding type rmsd covalent geometry : bond 0.01276 (14569) covalent geometry : angle 1.98407 (19753) SS BOND : bond 0.01718 ( 19) SS BOND : angle 3.27843 ( 38) hydrogen bonds : bond 0.16494 ( 630) hydrogen bonds : angle 8.85894 ( 1767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASN cc_start: 0.5332 (OUTLIER) cc_final: 0.5132 (p0) REVERT: A 427 MET cc_start: 0.7640 (ttp) cc_final: 0.7391 (ttm) REVERT: A 658 TYR cc_start: 0.2901 (t80) cc_final: 0.2697 (t80) REVERT: A 731 MET cc_start: 0.7010 (ppp) cc_final: 0.6416 (ppp) REVERT: B 231 HIS cc_start: 0.6932 (p-80) cc_final: 0.6692 (p-80) REVERT: B 270 PHE cc_start: 0.7576 (m-80) cc_final: 0.7309 (m-80) REVERT: B 303 MET cc_start: 0.7569 (mtp) cc_final: 0.7295 (mtm) REVERT: B 647 THR cc_start: 0.5902 (t) cc_final: 0.5241 (m) REVERT: B 745 ILE cc_start: 0.0922 (OUTLIER) cc_final: 0.0359 (mt) REVERT: B 759 TYR cc_start: 0.6294 (m-80) cc_final: 0.6020 (m-80) REVERT: B 786 TYR cc_start: 0.5327 (m-10) cc_final: 0.4978 (m-10) REVERT: B 835 MET cc_start: 0.0768 (ttp) cc_final: 0.0405 (ttp) REVERT: D 88 LEU cc_start: 0.6430 (tp) cc_final: 0.5755 (tp) outliers start: 35 outliers final: 15 residues processed: 298 average time/residue: 0.1256 time to fit residues: 53.8306 Evaluate side-chains 207 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 79 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 98 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 250 GLN A 377 GLN A 406 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 717 GLN A 776 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 387 ASN B 389 ASN B 426 ASN B 429 HIS B 513 GLN B 809 ASN D 3 GLN D 79 ASN D 84 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.150980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.128426 restraints weight = 31590.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130651 restraints weight = 60573.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.130904 restraints weight = 35160.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.131542 restraints weight = 22649.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.131955 restraints weight = 19242.651| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14588 Z= 0.177 Angle : 0.794 10.571 19791 Z= 0.417 Chirality : 0.047 0.249 2209 Planarity : 0.005 0.063 2502 Dihedral : 7.400 56.863 2022 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 3.73 % Allowed : 14.52 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.18), residues: 1802 helix: -1.02 (0.18), residues: 685 sheet: -2.64 (0.30), residues: 225 loop : -2.67 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 278 TYR 0.038 0.002 TYR A 672 PHE 0.038 0.002 PHE A 368 TRP 0.020 0.002 TRP B 468 HIS 0.011 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00385 (14569) covalent geometry : angle 0.79231 (19753) SS BOND : bond 0.00468 ( 19) SS BOND : angle 1.28142 ( 38) hydrogen bonds : bond 0.05766 ( 630) hydrogen bonds : angle 6.35259 ( 1767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 614 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.4095 (t80) REVERT: A 692 LYS cc_start: 0.1614 (tptm) cc_final: -0.0005 (tttm) REVERT: A 731 MET cc_start: 0.6869 (ppp) cc_final: 0.6215 (ppp) REVERT: B 116 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 427 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6713 (ttm) REVERT: B 727 MET cc_start: 0.4381 (mtt) cc_final: 0.3711 (ttt) REVERT: B 836 TYR cc_start: 0.0991 (OUTLIER) cc_final: -0.0911 (m-80) outliers start: 58 outliers final: 29 residues processed: 266 average time/residue: 0.1231 time to fit residues: 47.9194 Evaluate side-chains 216 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 97 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 250 GLN A 385 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 717 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 660 GLN C 79 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.148624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.121510 restraints weight = 31737.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.119560 restraints weight = 39375.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114588 restraints weight = 24911.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114249 restraints weight = 30450.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.114663 restraints weight = 28768.150| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14588 Z= 0.225 Angle : 0.780 9.513 19791 Z= 0.407 Chirality : 0.047 0.196 2209 Planarity : 0.005 0.059 2502 Dihedral : 6.980 52.139 2009 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.86 % Allowed : 18.44 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.67 (0.18), residues: 1802 helix: -0.65 (0.19), residues: 689 sheet: -2.31 (0.32), residues: 220 loop : -2.57 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 106 TYR 0.028 0.002 TYR A 672 PHE 0.017 0.002 PHE D 70 TRP 0.032 0.002 TRP D 107 HIS 0.008 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00511 (14569) covalent geometry : angle 0.77802 (19753) SS BOND : bond 0.00483 ( 19) SS BOND : angle 1.35737 ( 38) hydrogen bonds : bond 0.05766 ( 630) hydrogen bonds : angle 6.15958 ( 1767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 PHE cc_start: 0.5073 (OUTLIER) cc_final: 0.4780 (t80) REVERT: A 692 LYS cc_start: 0.0427 (tptm) cc_final: -0.0545 (tttm) REVERT: A 731 MET cc_start: 0.6904 (ppp) cc_final: 0.6338 (ppp) REVERT: B 116 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 330 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5712 (t80) outliers start: 60 outliers final: 32 residues processed: 245 average time/residue: 0.1179 time to fit residues: 42.3516 Evaluate side-chains 214 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 496 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.150205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.123155 restraints weight = 31446.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.119741 restraints weight = 38293.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.114928 restraints weight = 26001.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114863 restraints weight = 28086.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.115340 restraints weight = 25669.831| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14588 Z= 0.184 Angle : 0.720 8.797 19791 Z= 0.378 Chirality : 0.046 0.175 2209 Planarity : 0.005 0.058 2502 Dihedral : 6.650 51.923 2009 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.76 % Allowed : 19.22 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.35 (0.18), residues: 1802 helix: -0.30 (0.19), residues: 691 sheet: -2.20 (0.32), residues: 218 loop : -2.46 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 40 TYR 0.027 0.002 TYR A 672 PHE 0.015 0.002 PHE B 614 TRP 0.033 0.002 TRP B 570 HIS 0.008 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00409 (14569) covalent geometry : angle 0.71892 (19753) SS BOND : bond 0.00403 ( 19) SS BOND : angle 1.24831 ( 38) hydrogen bonds : bond 0.05386 ( 630) hydrogen bonds : angle 5.85883 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 202 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7510 (m) REVERT: A 208 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: A 692 LYS cc_start: 0.0166 (tptm) cc_final: -0.0696 (tttm) REVERT: A 724 LEU cc_start: 0.3225 (tt) cc_final: 0.2529 (mt) REVERT: A 731 MET cc_start: 0.6851 (ppp) cc_final: 0.6332 (ppp) REVERT: B 116 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7718 (tt) REVERT: B 330 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5551 (t80) REVERT: B 530 LYS cc_start: 0.1644 (OUTLIER) cc_final: 0.1361 (tmmt) REVERT: B 836 TYR cc_start: 0.0583 (OUTLIER) cc_final: -0.0942 (m-80) outliers start: 74 outliers final: 43 residues processed: 260 average time/residue: 0.1149 time to fit residues: 44.2905 Evaluate side-chains 231 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 176 GLN B 182 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124242 restraints weight = 31573.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.117705 restraints weight = 36122.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.117184 restraints weight = 35510.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.116925 restraints weight = 29687.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.117198 restraints weight = 24580.367| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14588 Z= 0.145 Angle : 0.682 12.524 19791 Z= 0.355 Chirality : 0.044 0.175 2209 Planarity : 0.005 0.058 2502 Dihedral : 6.182 53.324 2007 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.31 % Allowed : 21.08 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.05 (0.19), residues: 1802 helix: -0.02 (0.19), residues: 692 sheet: -2.09 (0.32), residues: 218 loop : -2.30 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.025 0.002 TYR A 672 PHE 0.031 0.001 PHE B 789 TRP 0.035 0.002 TRP B 570 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00312 (14569) covalent geometry : angle 0.68040 (19753) SS BOND : bond 0.00386 ( 19) SS BOND : angle 1.22172 ( 38) hydrogen bonds : bond 0.05019 ( 630) hydrogen bonds : angle 5.63543 ( 1767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7382 (m) REVERT: A 208 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: A 268 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6325 (tptt) REVERT: A 290 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 692 LYS cc_start: -0.0163 (tptm) cc_final: -0.1174 (tttt) REVERT: A 724 LEU cc_start: 0.2901 (tt) cc_final: 0.2410 (mt) REVERT: A 731 MET cc_start: 0.6977 (ppp) cc_final: 0.6524 (ppp) REVERT: B 116 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7828 (tt) REVERT: B 278 ARG cc_start: 0.6839 (mmm160) cc_final: 0.6463 (mmm-85) REVERT: B 330 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.5316 (t80) REVERT: B 427 MET cc_start: 0.6543 (ttm) cc_final: 0.6176 (ttm) REVERT: B 514 MET cc_start: 0.3645 (mmp) cc_final: 0.3159 (mpp) REVERT: B 836 TYR cc_start: 0.0325 (OUTLIER) cc_final: -0.1105 (m-80) REVERT: D 38 TRP cc_start: 0.6746 (m100) cc_final: 0.6205 (m100) outliers start: 67 outliers final: 37 residues processed: 258 average time/residue: 0.1179 time to fit residues: 44.3750 Evaluate side-chains 224 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 176 GLN B 182 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.149350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.122421 restraints weight = 31457.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.119509 restraints weight = 37180.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.115861 restraints weight = 25976.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.115852 restraints weight = 30618.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116671 restraints weight = 30505.659| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14588 Z= 0.193 Angle : 0.716 11.541 19791 Z= 0.371 Chirality : 0.045 0.170 2209 Planarity : 0.005 0.059 2502 Dihedral : 6.144 55.439 2003 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.21 % Allowed : 20.57 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.05 (0.19), residues: 1802 helix: -0.06 (0.19), residues: 698 sheet: -2.13 (0.32), residues: 220 loop : -2.26 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 40 TYR 0.023 0.002 TYR B 672 PHE 0.018 0.002 PHE B 789 TRP 0.038 0.002 TRP B 570 HIS 0.005 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00436 (14569) covalent geometry : angle 0.71474 (19753) SS BOND : bond 0.00423 ( 19) SS BOND : angle 1.17542 ( 38) hydrogen bonds : bond 0.05218 ( 630) hydrogen bonds : angle 5.61878 ( 1767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 190 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 208 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6854 (m-30) REVERT: A 268 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6359 (tptt) REVERT: A 290 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6633 (t80) REVERT: A 692 LYS cc_start: 0.0588 (tptm) cc_final: -0.0368 (tttt) REVERT: A 724 LEU cc_start: 0.3095 (tt) cc_final: 0.2535 (mt) REVERT: A 731 MET cc_start: 0.6984 (ppp) cc_final: 0.6462 (ppp) REVERT: A 817 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: B 116 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7828 (tt) REVERT: B 231 HIS cc_start: 0.6993 (p-80) cc_final: 0.6788 (p-80) REVERT: B 330 TYR cc_start: 0.6082 (OUTLIER) cc_final: 0.5740 (t80) REVERT: B 496 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.5944 (m90) REVERT: B 514 MET cc_start: 0.3185 (mmp) cc_final: 0.2880 (mpp) REVERT: D 38 TRP cc_start: 0.6543 (m100) cc_final: 0.5953 (m100) REVERT: D 82 TYR cc_start: 0.5835 (m-80) cc_final: 0.5526 (m-80) outliers start: 81 outliers final: 53 residues processed: 250 average time/residue: 0.1171 time to fit residues: 43.1443 Evaluate side-chains 244 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.0020 chunk 100 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 182 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS D 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.150898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124012 restraints weight = 31329.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117285 restraints weight = 35998.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116339 restraints weight = 37395.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.116796 restraints weight = 29853.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116438 restraints weight = 27722.971| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14588 Z= 0.154 Angle : 0.685 11.122 19791 Z= 0.356 Chirality : 0.044 0.178 2209 Planarity : 0.004 0.058 2502 Dihedral : 5.890 56.664 2001 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.24 % Allowed : 22.04 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.90 (0.19), residues: 1802 helix: 0.08 (0.20), residues: 698 sheet: -2.06 (0.32), residues: 220 loop : -2.19 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 40 TYR 0.023 0.002 TYR A 672 PHE 0.040 0.002 PHE B 789 TRP 0.050 0.002 TRP D 107 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00338 (14569) covalent geometry : angle 0.68431 (19753) SS BOND : bond 0.00376 ( 19) SS BOND : angle 1.11126 ( 38) hydrogen bonds : bond 0.04967 ( 630) hydrogen bonds : angle 5.51973 ( 1767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7321 (m) REVERT: A 208 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: A 290 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 521 ARG cc_start: 0.4812 (ttt90) cc_final: 0.4354 (mtp180) REVERT: A 692 LYS cc_start: 0.0326 (tptm) cc_final: -0.0557 (tttt) REVERT: A 724 LEU cc_start: 0.3000 (tt) cc_final: 0.2482 (mt) REVERT: A 830 MET cc_start: 0.5186 (mmt) cc_final: 0.4859 (mmt) REVERT: B 116 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 278 ARG cc_start: 0.6814 (mmm160) cc_final: 0.6461 (mmm160) REVERT: B 306 LEU cc_start: 0.7771 (tp) cc_final: 0.7479 (tp) REVERT: B 330 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.5460 (t80) REVERT: B 427 MET cc_start: 0.6555 (ttm) cc_final: 0.6235 (ttm) REVERT: B 496 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.6032 (m90) REVERT: B 514 MET cc_start: 0.3412 (mmp) cc_final: 0.3098 (mpp) REVERT: B 570 TRP cc_start: 0.5409 (p-90) cc_final: 0.4899 (t60) REVERT: B 740 LYS cc_start: 0.5534 (mptt) cc_final: 0.5242 (pttp) REVERT: D 38 TRP cc_start: 0.6630 (m100) cc_final: 0.6254 (m100) outliers start: 66 outliers final: 46 residues processed: 251 average time/residue: 0.1130 time to fit residues: 42.4285 Evaluate side-chains 243 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 96 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.150394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.123776 restraints weight = 31411.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.121707 restraints weight = 38292.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117012 restraints weight = 23476.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.116981 restraints weight = 31300.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117158 restraints weight = 26865.163| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14588 Z= 0.169 Angle : 0.699 11.932 19791 Z= 0.362 Chirality : 0.044 0.172 2209 Planarity : 0.004 0.059 2502 Dihedral : 5.858 58.145 2001 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.24 % Allowed : 22.24 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.86 (0.19), residues: 1802 helix: 0.13 (0.20), residues: 701 sheet: -2.17 (0.31), residues: 232 loop : -2.14 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 40 TYR 0.022 0.002 TYR B 672 PHE 0.018 0.001 PHE B 614 TRP 0.038 0.002 TRP B 570 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00382 (14569) covalent geometry : angle 0.69829 (19753) SS BOND : bond 0.00385 ( 19) SS BOND : angle 1.11376 ( 38) hydrogen bonds : bond 0.04977 ( 630) hydrogen bonds : angle 5.50674 ( 1767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7342 (m) REVERT: A 208 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: A 290 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7372 (t80) REVERT: A 521 ARG cc_start: 0.4852 (ttt90) cc_final: 0.4369 (mtp180) REVERT: A 692 LYS cc_start: 0.0680 (tptm) cc_final: -0.0255 (tttt) REVERT: A 724 LEU cc_start: 0.3049 (tt) cc_final: 0.2503 (mt) REVERT: A 731 MET cc_start: 0.6812 (ppp) cc_final: 0.6326 (ppp) REVERT: B 116 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7645 (tt) REVERT: B 278 ARG cc_start: 0.6684 (mmm160) cc_final: 0.6300 (mmm-85) REVERT: B 330 TYR cc_start: 0.5896 (OUTLIER) cc_final: 0.5670 (t80) REVERT: B 496 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.5956 (m90) REVERT: B 727 MET cc_start: 0.5339 (mtt) cc_final: 0.3555 (ttm) REVERT: B 740 LYS cc_start: 0.5500 (mptt) cc_final: 0.5188 (pttp) REVERT: D 38 TRP cc_start: 0.6663 (m100) cc_final: 0.6360 (m100) REVERT: D 88 LEU cc_start: 0.5635 (tp) cc_final: 0.5260 (tp) outliers start: 66 outliers final: 52 residues processed: 247 average time/residue: 0.1113 time to fit residues: 40.9758 Evaluate side-chains 250 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 102 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.150009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.123045 restraints weight = 31522.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.117363 restraints weight = 37111.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.116740 restraints weight = 32091.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.116605 restraints weight = 27630.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116537 restraints weight = 25411.558| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14588 Z= 0.178 Angle : 0.702 10.398 19791 Z= 0.362 Chirality : 0.044 0.175 2209 Planarity : 0.005 0.059 2502 Dihedral : 5.876 59.512 2001 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.18 % Allowed : 22.56 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.88 (0.19), residues: 1802 helix: 0.10 (0.20), residues: 704 sheet: -2.22 (0.31), residues: 213 loop : -2.15 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 40 TYR 0.023 0.002 TYR B 672 PHE 0.019 0.001 PHE B 614 TRP 0.042 0.002 TRP B 570 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00401 (14569) covalent geometry : angle 0.69995 (19753) SS BOND : bond 0.00395 ( 19) SS BOND : angle 1.31773 ( 38) hydrogen bonds : bond 0.05027 ( 630) hydrogen bonds : angle 5.53387 ( 1767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7401 (m) REVERT: A 208 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: A 290 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7359 (t80) REVERT: A 692 LYS cc_start: 0.0577 (tptm) cc_final: -0.0334 (tttt) REVERT: A 724 LEU cc_start: 0.3096 (tt) cc_final: 0.2517 (mt) REVERT: A 731 MET cc_start: 0.7065 (ppp) cc_final: 0.6593 (ppp) REVERT: A 733 ILE cc_start: 0.5381 (tt) cc_final: 0.5175 (tp) REVERT: A 830 MET cc_start: 0.4470 (mmt) cc_final: 0.3766 (tpt) REVERT: B 116 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 330 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.5640 (t80) REVERT: B 427 MET cc_start: 0.6337 (ttm) cc_final: 0.6114 (ttm) REVERT: B 496 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.5855 (m90) REVERT: B 570 TRP cc_start: 0.5350 (p-90) cc_final: 0.4799 (t60) REVERT: B 740 LYS cc_start: 0.5513 (mptt) cc_final: 0.5212 (pttp) REVERT: D 38 TRP cc_start: 0.6800 (m100) cc_final: 0.6426 (m100) REVERT: D 78 LYS cc_start: 0.5485 (pttm) cc_final: 0.5043 (tppt) REVERT: D 88 LEU cc_start: 0.5781 (tp) cc_final: 0.5375 (tp) outliers start: 65 outliers final: 51 residues processed: 245 average time/residue: 0.1120 time to fit residues: 40.7253 Evaluate side-chains 246 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.151649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.124808 restraints weight = 31400.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.122083 restraints weight = 38599.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118897 restraints weight = 25677.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.118106 restraints weight = 29430.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.118691 restraints weight = 28444.584| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14588 Z= 0.169 Angle : 0.710 10.330 19791 Z= 0.366 Chirality : 0.045 0.234 2209 Planarity : 0.005 0.058 2502 Dihedral : 5.791 57.769 2001 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.79 % Allowed : 23.07 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.87 (0.19), residues: 1802 helix: 0.14 (0.20), residues: 702 sheet: -2.31 (0.30), residues: 225 loop : -2.12 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 40 TYR 0.024 0.002 TYR B 672 PHE 0.020 0.001 PHE B 614 TRP 0.074 0.002 TRP D 107 HIS 0.005 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00379 (14569) covalent geometry : angle 0.70756 (19753) SS BOND : bond 0.00368 ( 19) SS BOND : angle 1.43126 ( 38) hydrogen bonds : bond 0.04993 ( 630) hydrogen bonds : angle 5.51769 ( 1767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 188 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7298 (m) REVERT: A 208 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6738 (m-30) REVERT: A 290 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7296 (t80) REVERT: A 692 LYS cc_start: 0.0900 (tptm) cc_final: -0.0117 (tttt) REVERT: A 724 LEU cc_start: 0.3075 (tt) cc_final: 0.2512 (mt) REVERT: A 830 MET cc_start: 0.4289 (mmt) cc_final: 0.3592 (tpt) REVERT: B 116 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7646 (tt) REVERT: B 278 ARG cc_start: 0.6653 (mmm160) cc_final: 0.6229 (mmm-85) REVERT: B 330 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.5637 (t80) REVERT: B 496 HIS cc_start: 0.6543 (OUTLIER) cc_final: 0.5754 (m90) REVERT: B 727 MET cc_start: 0.5422 (mtt) cc_final: 0.3625 (ttm) REVERT: B 740 LYS cc_start: 0.5509 (mptt) cc_final: 0.5245 (pttp) REVERT: C 40 ARG cc_start: 0.6286 (ttt180) cc_final: 0.5989 (ttt180) REVERT: D 38 TRP cc_start: 0.6641 (m100) cc_final: 0.6414 (m100) REVERT: D 88 LEU cc_start: 0.5977 (tp) cc_final: 0.5647 (tp) outliers start: 59 outliers final: 50 residues processed: 238 average time/residue: 0.1242 time to fit residues: 43.8631 Evaluate side-chains 240 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 142 optimal weight: 0.0030 chunk 149 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.150391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.123702 restraints weight = 31458.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.116854 restraints weight = 36949.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.116552 restraints weight = 33889.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116471 restraints weight = 29204.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116615 restraints weight = 24661.849| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.249 14588 Z= 0.258 Angle : 0.899 59.200 19791 Z= 0.503 Chirality : 0.047 0.770 2209 Planarity : 0.005 0.058 2502 Dihedral : 5.753 57.771 1999 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.98 % Allowed : 23.01 % Favored : 73.01 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.71 % 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: -1.87 (0.19), residues: 1802 helix: 0.13 (0.20), residues: 702 sheet: -2.30 (0.30), residues: 225 loop : -2.12 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.026 0.002 TYR B 792 PHE 0.017 0.001 PHE B 614 TRP 0.062 0.002 TRP D 107 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00554 (14569) covalent geometry : angle 0.89776 (19753) SS BOND : bond 0.00355 ( 19) SS BOND : angle 1.40868 ( 38) hydrogen bonds : bond 0.05007 ( 630) hydrogen bonds : angle 5.52578 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.07 seconds wall clock time: 51 minutes 31.78 seconds (3091.78 seconds total)