Starting phenix.real_space_refine on Thu Sep 18 19:49:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgz_19163/09_2025/8rgz_19163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgz_19163/09_2025/8rgz_19163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rgz_19163/09_2025/8rgz_19163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgz_19163/09_2025/8rgz_19163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rgz_19163/09_2025/8rgz_19163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgz_19163/09_2025/8rgz_19163.map" } resolution = 3.27 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 93 5.16 5 C 12387 2.51 5 N 3384 2.21 5 O 3681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19545 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Time building chain proxies: 4.13, per 1000 atoms: 0.21 Number of scatterers: 19545 At special positions: 0 Unit cell: (184.127, 168.676, 159.662, 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 93 16.00 O 3681 8.00 N 3384 7.00 C 12387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.06 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.13 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.02 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 116 " distance=2.06 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.15 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.06 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.16 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.02 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 116 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 116 " distance=2.04 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.02 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 112 " distance=2.02 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: 1.67 Conformation dependent library (CDL) restraints added in 751.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 52 sheets defined 17.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.695A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.203A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 690 through 698 removed outlier: 3.789A pdb=" N GLY A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.507A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.363A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.899A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 698 removed outlier: 3.962A pdb=" N GLY B 698 " --> pdb=" O ILE B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 711 removed outlier: 3.531A pdb=" N LEU B 711 " --> pdb=" O ARG B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 429 removed outlier: 4.220A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.681A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.645A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 Processing helix chain 'C' and resid 690 through 698 removed outlier: 4.050A pdb=" N GLY C 698 " --> pdb=" O ILE C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 711 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'G' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.182A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.155A pdb=" N MET A 568 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 125 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.544A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.544A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 191 removed outlier: 6.027A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.327A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 319 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 214 Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.132A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.740A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 125 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 568 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.520A pdb=" N SER D 54 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 55 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS D 71 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP D 57 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AB8, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.979A pdb=" N GLY E 108 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E 57 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR E 73 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.979A pdb=" N GLY E 108 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER E 121 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.978A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.502A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.502A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 180 through 191 removed outlier: 5.900A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.130A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG B 342 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP B 323 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 344 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN B 321 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 346 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 319 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC7, first strand: chain 'B' and resid 210 through 214 Processing sheet with id=AC8, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC9, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD1, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.761A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.842A pdb=" N VAL C 125 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET C 568 " --> pdb=" O VAL C 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.695A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 601 " --> pdb=" O GLN C 584 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.498A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.498A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 180 through 191 removed outlier: 6.190A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.199A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD9, first strand: chain 'C' and resid 210 through 214 Processing sheet with id=AE1, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AE2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AE3, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.401A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AE5, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AE6, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.630A pdb=" N SER H 54 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL H 55 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS H 71 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP H 57 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AE8, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AE9, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.752A pdb=" N SER F 54 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 55 " --> pdb=" O HIS F 71 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS F 71 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP F 57 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 30 through 31 removed outlier: 4.175A pdb=" N TYR F 130 " --> pdb=" O ARG F 118 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 23 through 26 Processing sheet with id=AF3, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.714A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.714A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AF6, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.037A pdb=" N GLY G 108 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU G 57 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR G 73 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.037A pdb=" N GLY G 108 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2325 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: 4.26 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3173 1.30 - 1.44: 5888 1.44 - 1.57: 10847 1.57 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 20052 Sorted by residual: bond pdb=" CE1 HIS B 681 " pdb=" NE2 HIS B 681 " ideal model delta sigma weight residual 1.321 1.411 -0.090 1.00e-02 1.00e+04 8.18e+01 bond pdb=" C THR C 690 " pdb=" N ARG C 691 " ideal model delta sigma weight residual 1.335 1.438 -0.104 1.25e-02 6.40e+03 6.88e+01 bond pdb=" CE1 HIS A 681 " pdb=" NE2 HIS A 681 " ideal model delta sigma weight residual 1.321 1.401 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" CE1 HIS A 712 " pdb=" NE2 HIS A 712 " ideal model delta sigma weight residual 1.321 1.400 -0.079 1.00e-02 1.00e+04 6.31e+01 bond pdb=" CE1 HIS C 681 " pdb=" NE2 HIS C 681 " ideal model delta sigma weight residual 1.321 1.391 -0.070 1.00e-02 1.00e+04 4.94e+01 ... (remaining 20047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 24133 1.65 - 3.30: 2813 3.30 - 4.96: 269 4.96 - 6.61: 44 6.61 - 8.26: 8 Bond angle restraints: 27267 Sorted by residual: angle pdb=" N ILE B 719 " pdb=" CA ILE B 719 " pdb=" C ILE B 719 " ideal model delta sigma weight residual 110.42 117.40 -6.98 9.60e-01 1.09e+00 5.29e+01 angle pdb=" OD1 ASN B 217 " pdb=" CG ASN B 217 " pdb=" ND2 ASN B 217 " ideal model delta sigma weight residual 122.60 116.61 5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" O THR C 690 " pdb=" C THR C 690 " pdb=" N ARG C 691 " ideal model delta sigma weight residual 122.79 129.09 -6.30 1.14e+00 7.69e-01 3.06e+01 angle pdb=" N VAL B 352 " pdb=" CA VAL B 352 " pdb=" CB VAL B 352 " ideal model delta sigma weight residual 111.41 117.72 -6.31 1.38e+00 5.25e-01 2.09e+01 angle pdb=" OD1 ASN A 217 " pdb=" CG ASN A 217 " pdb=" ND2 ASN A 217 " ideal model delta sigma weight residual 122.60 118.04 4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 27262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10928 17.76 - 35.51: 781 35.51 - 53.27: 154 53.27 - 71.02: 52 71.02 - 88.78: 16 Dihedral angle restraints: 11931 sinusoidal: 4779 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 633 " pdb=" CB CYS A 633 " ideal model delta sinusoidal sigma weight residual -86.00 -174.78 88.78 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS G 42 " pdb=" SG CYS G 42 " pdb=" SG CYS G 112 " pdb=" CB CYS G 112 " ideal model delta sinusoidal sigma weight residual 93.00 128.98 -35.98 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA THR E 26 " pdb=" C THR E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta harmonic sigma weight residual 0.00 -20.22 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2029 0.070 - 0.139: 810 0.139 - 0.209: 115 0.209 - 0.278: 11 0.278 - 0.348: 2 Chirality restraints: 2967 Sorted by residual: chirality pdb=" CA PRO H 125 " pdb=" N PRO H 125 " pdb=" C PRO H 125 " pdb=" CB PRO H 125 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PRO F 125 " pdb=" N PRO F 125 " pdb=" C PRO F 125 " pdb=" CB PRO F 125 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PRO B 193 " pdb=" N PRO B 193 " pdb=" C PRO B 193 " pdb=" CB PRO B 193 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2964 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 528 " -0.069 2.00e-02 2.50e+03 4.47e-02 5.00e+01 pdb=" CG TRP C 528 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP C 528 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 528 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP C 528 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP C 528 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP C 528 " 0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 528 " -0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 528 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 528 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 528 " -0.088 2.00e-02 2.50e+03 4.44e-02 4.93e+01 pdb=" CG TRP B 528 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 528 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP B 528 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP B 528 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP B 528 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP B 528 " 0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 528 " -0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 528 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 528 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 73 " 0.021 2.00e-02 2.50e+03 4.23e-02 4.46e+01 pdb=" CG TRP D 73 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 73 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 73 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP D 73 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP D 73 " -0.077 2.00e-02 2.50e+03 pdb=" CE3 TRP D 73 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 73 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 73 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP D 73 " 0.054 2.00e-02 2.50e+03 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1811 2.74 - 3.28: 19014 3.28 - 3.82: 33297 3.82 - 4.36: 42250 4.36 - 4.90: 71195 Nonbonded interactions: 167567 Sorted by model distance: nonbonded pdb=" OH TYR A 303 " pdb=" OD2 ASP D 77 " model vdw 2.198 3.040 nonbonded pdb=" O TRP C 528 " pdb=" NE2 GLN C 532 " model vdw 2.209 3.120 nonbonded pdb=" O GLN A 321 " pdb=" OH TYR D 79 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 392 " pdb=" NE2 HIS C 681 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR B 665 " pdb=" O VAL C 124 " model vdw 2.219 3.040 ... (remaining 167562 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.011 0.131 20073 Z= 0.688 Angle : 1.100 8.259 27309 Z= 0.708 Chirality : 0.070 0.348 2967 Planarity : 0.011 0.140 3519 Dihedral : 13.473 82.745 7284 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.19 % Allowed : 1.83 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.38 (0.17), residues: 2418 helix: -0.90 (0.26), residues: 321 sheet: -0.16 (0.16), residues: 930 loop : 0.05 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.003 ARG B 505 TYR 0.061 0.010 TYR C 157 PHE 0.066 0.010 PHE B 300 TRP 0.088 0.016 TRP B 528 HIS 0.035 0.006 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.01057 (20052) covalent geometry : angle 1.09613 (27267) SS BOND : bond 0.04623 ( 21) SS BOND : angle 2.47811 ( 42) hydrogen bonds : bond 0.13583 ( 761) hydrogen bonds : angle 7.77606 ( 2325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 412 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8909 (mt-10) REVERT: A 384 PHE cc_start: 0.8236 (m-10) cc_final: 0.7928 (m-80) REVERT: A 502 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8791 (mp0) REVERT: A 562 ARG cc_start: 0.7888 (ttt180) cc_final: 0.7597 (mtm110) REVERT: A 638 ARG cc_start: 0.7674 (mtp-110) cc_final: 0.7001 (mtm110) REVERT: A 649 TYR cc_start: 0.7400 (t80) cc_final: 0.6855 (t80) REVERT: D 106 MET cc_start: 0.6896 (mmt) cc_final: 0.6538 (mmm) REVERT: D 110 ASP cc_start: 0.7528 (m-30) cc_final: 0.6406 (m-30) REVERT: D 126 TYR cc_start: 0.8672 (p90) cc_final: 0.8375 (p90) REVERT: E 22 VAL cc_start: 0.8410 (t) cc_final: 0.8196 (p) REVERT: B 317 ASP cc_start: 0.9089 (m-30) cc_final: 0.8681 (t0) REVERT: B 529 CYS cc_start: 0.8425 (m) cc_final: 0.8140 (t) REVERT: B 587 MET cc_start: 0.5993 (mmm) cc_final: 0.5557 (mmm) REVERT: C 112 ASN cc_start: 0.7176 (t0) cc_final: 0.6754 (t0) REVERT: C 142 TYR cc_start: 0.8559 (m-80) cc_final: 0.8133 (m-80) REVERT: C 188 ASP cc_start: 0.9190 (t0) cc_final: 0.8768 (t0) REVERT: C 220 THR cc_start: 0.9089 (p) cc_final: 0.8818 (p) REVERT: C 297 MET cc_start: 0.9208 (ttm) cc_final: 0.8849 (ttp) REVERT: C 562 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7733 (ttp80) REVERT: C 563 MET cc_start: 0.6341 (mmm) cc_final: 0.6075 (mmp) REVERT: C 675 ILE cc_start: 0.8463 (mm) cc_final: 0.8258 (mm) REVERT: H 57 TRP cc_start: 0.8564 (m100) cc_final: 0.8353 (m100) REVERT: H 68 TRP cc_start: 0.8171 (t60) cc_final: 0.7956 (t60) REVERT: H 80 TYR cc_start: 0.8173 (m-80) cc_final: 0.7923 (m-10) REVERT: H 106 MET cc_start: 0.8189 (mmt) cc_final: 0.7913 (mmt) REVERT: F 77 ASP cc_start: 0.8988 (t0) cc_final: 0.8641 (t0) REVERT: F 78 LYS cc_start: 0.8972 (mttt) cc_final: 0.8445 (mttt) REVERT: F 80 TYR cc_start: 0.8657 (m-80) cc_final: 0.8443 (m-10) REVERT: F 120 TYR cc_start: 0.8263 (m-80) cc_final: 0.8037 (m-80) REVERT: L 72 ILE cc_start: 0.9059 (mm) cc_final: 0.8819 (mt) REVERT: G 46 GLN cc_start: 0.7496 (mt0) cc_final: 0.7230 (mp10) outliers start: 4 outliers final: 2 residues processed: 413 average time/residue: 0.1680 time to fit residues: 102.1464 Evaluate side-chains 325 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain C residue 154 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 217 ASN A 255 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 217 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 616 GLN C 709 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115908 restraints weight = 28215.666| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.39 r_work: 0.3211 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 20073 Z= 0.227 Angle : 0.623 15.457 27309 Z= 0.331 Chirality : 0.044 0.156 2967 Planarity : 0.005 0.057 3519 Dihedral : 4.876 59.557 2738 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.60 % Allowed : 9.26 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.27 (0.17), residues: 2418 helix: -0.51 (0.27), residues: 324 sheet: -0.17 (0.17), residues: 897 loop : 0.10 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 132 TYR 0.019 0.002 TYR B 213 PHE 0.019 0.002 PHE A 159 TRP 0.013 0.001 TRP A 354 HIS 0.012 0.002 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00517 (20052) covalent geometry : angle 0.61425 (27267) SS BOND : bond 0.00375 ( 21) SS BOND : angle 2.77439 ( 42) hydrogen bonds : bond 0.04385 ( 761) hydrogen bonds : angle 6.13981 ( 2325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.7698 (mmp) cc_final: 0.6935 (mmt) REVERT: A 562 ARG cc_start: 0.8009 (ttt180) cc_final: 0.7466 (mtm110) REVERT: A 638 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6711 (mtm110) REVERT: A 649 TYR cc_start: 0.7006 (t80) cc_final: 0.6091 (t80) REVERT: D 110 ASP cc_start: 0.6575 (m-30) cc_final: 0.5674 (m-30) REVERT: B 140 GLN cc_start: 0.6598 (tt0) cc_final: 0.6269 (tt0) REVERT: B 374 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6851 (tm-30) REVERT: B 562 ARG cc_start: 0.6731 (ptt90) cc_final: 0.6351 (ptt90) REVERT: B 587 MET cc_start: 0.7196 (mmm) cc_final: 0.6737 (mmm) REVERT: B 678 LEU cc_start: 0.8777 (tp) cc_final: 0.8556 (tp) REVERT: C 112 ASN cc_start: 0.7258 (t0) cc_final: 0.6673 (t0) REVERT: C 228 HIS cc_start: 0.8424 (m90) cc_final: 0.8148 (m90) REVERT: C 385 ARG cc_start: 0.8367 (mpt180) cc_final: 0.7752 (mtp85) REVERT: C 562 ARG cc_start: 0.7675 (ptt-90) cc_final: 0.7242 (ttp80) REVERT: H 130 TYR cc_start: 0.8842 (m-80) cc_final: 0.8526 (m-10) REVERT: F 64 LYS cc_start: 0.8375 (mptt) cc_final: 0.7479 (tmmt) REVERT: F 68 TRP cc_start: 0.8164 (t60) cc_final: 0.7869 (t60) REVERT: F 78 LYS cc_start: 0.8892 (mttt) cc_final: 0.8405 (mttt) REVERT: L 98 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7361 (mttm) REVERT: G 46 GLN cc_start: 0.7977 (mt0) cc_final: 0.7685 (mp10) outliers start: 34 outliers final: 22 residues processed: 363 average time/residue: 0.1580 time to fit residues: 85.9973 Evaluate side-chains 330 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 307 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 117 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 236 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN D 35 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN G 117 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114759 restraints weight = 28396.483| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.34 r_work: 0.3189 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20073 Z= 0.218 Angle : 0.590 9.895 27309 Z= 0.313 Chirality : 0.044 0.164 2967 Planarity : 0.005 0.054 3519 Dihedral : 4.638 18.553 2733 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.16 % Allowed : 11.71 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.24 (0.17), residues: 2418 helix: -0.39 (0.26), residues: 327 sheet: -0.10 (0.17), residues: 867 loop : 0.04 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 101 TYR 0.029 0.002 TYR B 689 PHE 0.017 0.002 PHE A 159 TRP 0.012 0.001 TRP A 354 HIS 0.013 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00494 (20052) covalent geometry : angle 0.58678 (27267) SS BOND : bond 0.00314 ( 21) SS BOND : angle 1.62338 ( 42) hydrogen bonds : bond 0.04012 ( 761) hydrogen bonds : angle 5.91510 ( 2325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 GLN cc_start: 0.6805 (tt0) cc_final: 0.6348 (tt0) REVERT: B 317 ASP cc_start: 0.8619 (p0) cc_final: 0.8311 (m-30) REVERT: B 374 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6883 (tm-30) REVERT: B 562 ARG cc_start: 0.6625 (ptt90) cc_final: 0.6351 (ptt90) REVERT: B 587 MET cc_start: 0.7189 (mmm) cc_final: 0.6609 (mmm) REVERT: B 622 GLU cc_start: 0.7257 (tt0) cc_final: 0.6814 (tt0) REVERT: C 112 ASN cc_start: 0.7257 (t0) cc_final: 0.6727 (t0) REVERT: C 562 ARG cc_start: 0.7791 (ptt-90) cc_final: 0.7235 (ttp80) REVERT: C 709 ASN cc_start: 0.8655 (m-40) cc_final: 0.8425 (m110) REVERT: H 130 TYR cc_start: 0.8803 (m-80) cc_final: 0.8506 (m-10) REVERT: F 43 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: F 64 LYS cc_start: 0.8358 (mptt) cc_final: 0.7473 (tmtt) REVERT: F 78 LYS cc_start: 0.8899 (mttt) cc_final: 0.8466 (mttt) REVERT: L 98 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7416 (mttm) REVERT: G 46 GLN cc_start: 0.8145 (mt0) cc_final: 0.7748 (mp10) outliers start: 46 outliers final: 31 residues processed: 351 average time/residue: 0.1634 time to fit residues: 85.9725 Evaluate side-chains 340 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 158 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN G 77 ASN G 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116119 restraints weight = 28173.652| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.35 r_work: 0.3211 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20073 Z= 0.165 Angle : 0.560 11.096 27309 Z= 0.298 Chirality : 0.043 0.160 2967 Planarity : 0.005 0.052 3519 Dihedral : 4.537 19.626 2733 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.49 % Allowed : 13.12 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.16 (0.17), residues: 2418 helix: -0.34 (0.26), residues: 330 sheet: -0.06 (0.18), residues: 867 loop : 0.11 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 101 TYR 0.021 0.001 TYR A 649 PHE 0.026 0.002 PHE A 641 TRP 0.011 0.001 TRP B 354 HIS 0.011 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00372 (20052) covalent geometry : angle 0.55251 (27267) SS BOND : bond 0.00367 ( 21) SS BOND : angle 2.32124 ( 42) hydrogen bonds : bond 0.03735 ( 761) hydrogen bonds : angle 5.71242 ( 2325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 329 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.7751 (mmp) cc_final: 0.6652 (mmt) REVERT: A 638 ARG cc_start: 0.7466 (mtp-110) cc_final: 0.7234 (mtp-110) REVERT: A 677 MET cc_start: 0.8369 (mmt) cc_final: 0.8048 (mmp) REVERT: E 93 THR cc_start: 0.8278 (p) cc_final: 0.8060 (t) REVERT: B 140 GLN cc_start: 0.6767 (tt0) cc_final: 0.6261 (tt0) REVERT: B 317 ASP cc_start: 0.8621 (p0) cc_final: 0.8258 (m-30) REVERT: B 374 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6859 (tm-30) REVERT: B 562 ARG cc_start: 0.6580 (ptt90) cc_final: 0.6343 (ptt90) REVERT: B 587 MET cc_start: 0.7193 (mmm) cc_final: 0.6478 (mmm) REVERT: B 622 GLU cc_start: 0.7126 (tt0) cc_final: 0.6675 (tt0) REVERT: C 112 ASN cc_start: 0.7260 (t0) cc_final: 0.6738 (t0) REVERT: C 195 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: C 208 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.7854 (mtp85) REVERT: C 562 ARG cc_start: 0.7796 (ptt-90) cc_final: 0.7209 (ttp80) REVERT: C 709 ASN cc_start: 0.8699 (m-40) cc_final: 0.8457 (m110) REVERT: C 714 LEU cc_start: 0.8257 (mt) cc_final: 0.8000 (mt) REVERT: H 24 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8413 (ttpp) REVERT: H 130 TYR cc_start: 0.8702 (m-80) cc_final: 0.8491 (m-10) REVERT: F 43 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: F 78 LYS cc_start: 0.8908 (mttt) cc_final: 0.8494 (mttt) REVERT: L 98 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7454 (mttm) REVERT: G 46 GLN cc_start: 0.8127 (mt0) cc_final: 0.7720 (mp10) outliers start: 53 outliers final: 32 residues processed: 355 average time/residue: 0.1684 time to fit residues: 89.0681 Evaluate side-chains 337 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 186 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114692 restraints weight = 28350.974| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.35 r_work: 0.3180 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20073 Z= 0.220 Angle : 0.578 9.547 27309 Z= 0.308 Chirality : 0.044 0.215 2967 Planarity : 0.005 0.048 3519 Dihedral : 4.585 20.011 2733 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.06 % Allowed : 13.73 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.27 (0.17), residues: 2418 helix: -0.32 (0.27), residues: 324 sheet: -0.22 (0.18), residues: 834 loop : 0.06 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 43 TYR 0.024 0.002 TYR A 164 PHE 0.017 0.002 PHE C 650 TRP 0.011 0.001 TRP B 354 HIS 0.012 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00500 (20052) covalent geometry : angle 0.57384 (27267) SS BOND : bond 0.00303 ( 21) SS BOND : angle 1.89620 ( 42) hydrogen bonds : bond 0.03775 ( 761) hydrogen bonds : angle 5.72957 ( 2325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.7791 (mmp) cc_final: 0.6672 (mmt) REVERT: A 536 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7666 (tt) REVERT: A 638 ARG cc_start: 0.7537 (mtp-110) cc_final: 0.7235 (mtp-110) REVERT: E 93 THR cc_start: 0.8255 (p) cc_final: 0.8028 (t) REVERT: B 140 GLN cc_start: 0.6650 (tt0) cc_final: 0.6195 (tt0) REVERT: B 374 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6912 (tm-30) REVERT: B 375 MET cc_start: 0.8542 (ttt) cc_final: 0.8306 (ttt) REVERT: B 562 ARG cc_start: 0.6555 (ptt90) cc_final: 0.6126 (ptt90) REVERT: B 587 MET cc_start: 0.7187 (mmm) cc_final: 0.6431 (mmm) REVERT: B 622 GLU cc_start: 0.7148 (tt0) cc_final: 0.6670 (tt0) REVERT: C 112 ASN cc_start: 0.7399 (t0) cc_final: 0.6876 (t0) REVERT: C 195 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: C 208 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.7857 (mtp85) REVERT: C 562 ARG cc_start: 0.7923 (ptt-90) cc_final: 0.7337 (ttp80) REVERT: C 709 ASN cc_start: 0.8691 (m-40) cc_final: 0.8472 (m110) REVERT: H 24 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8482 (ttpp) REVERT: H 130 TYR cc_start: 0.8814 (m-80) cc_final: 0.8571 (m-10) REVERT: H 135 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8805 (p) REVERT: F 43 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: F 78 LYS cc_start: 0.8914 (mttt) cc_final: 0.8532 (mttt) REVERT: L 98 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7513 (mttm) REVERT: G 21 ILE cc_start: 0.8261 (mm) cc_final: 0.7827 (mt) REVERT: G 46 GLN cc_start: 0.8152 (mt0) cc_final: 0.7749 (mp10) outliers start: 65 outliers final: 43 residues processed: 359 average time/residue: 0.1565 time to fit residues: 85.0022 Evaluate side-chains 354 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 70 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112422 restraints weight = 28499.809| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.37 r_work: 0.3148 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 20073 Z= 0.318 Angle : 0.646 10.776 27309 Z= 0.344 Chirality : 0.046 0.242 2967 Planarity : 0.005 0.048 3519 Dihedral : 4.860 18.829 2733 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.24 % Allowed : 14.62 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.60 (0.17), residues: 2418 helix: -0.81 (0.26), residues: 342 sheet: -0.33 (0.18), residues: 858 loop : -0.16 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 43 TYR 0.027 0.002 TYR A 164 PHE 0.020 0.002 PHE A 159 TRP 0.012 0.002 TRP A 354 HIS 0.013 0.002 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00727 (20052) covalent geometry : angle 0.64231 (27267) SS BOND : bond 0.00483 ( 21) SS BOND : angle 1.80814 ( 42) hydrogen bonds : bond 0.04137 ( 761) hydrogen bonds : angle 5.94245 ( 2325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 313 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.8043 (m-80) cc_final: 0.7785 (m-80) REVERT: A 520 MET cc_start: 0.7884 (mmp) cc_final: 0.7535 (mmt) REVERT: A 536 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 562 ARG cc_start: 0.7862 (ttt90) cc_final: 0.6991 (ttp80) REVERT: E 93 THR cc_start: 0.8359 (p) cc_final: 0.8081 (t) REVERT: E 124 GLN cc_start: 0.8404 (mp10) cc_final: 0.7748 (mm-40) REVERT: B 140 GLN cc_start: 0.6731 (tt0) cc_final: 0.6281 (tt0) REVERT: B 374 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6976 (tm-30) REVERT: B 375 MET cc_start: 0.8634 (ttt) cc_final: 0.8371 (ttt) REVERT: B 562 ARG cc_start: 0.6445 (ptt90) cc_final: 0.6157 (ptt90) REVERT: B 587 MET cc_start: 0.7298 (mmm) cc_final: 0.6559 (mmm) REVERT: C 112 ASN cc_start: 0.7319 (t0) cc_final: 0.6827 (t0) REVERT: C 195 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8580 (pm20) REVERT: C 208 ARG cc_start: 0.8389 (mtt-85) cc_final: 0.7862 (mtp85) REVERT: C 562 ARG cc_start: 0.8149 (ptt-90) cc_final: 0.7569 (ttp80) REVERT: C 709 ASN cc_start: 0.8741 (m-40) cc_final: 0.8514 (m110) REVERT: H 32 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7686 (mmmt) REVERT: H 135 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8756 (p) REVERT: F 43 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: F 78 LYS cc_start: 0.8913 (mttt) cc_final: 0.8558 (mttt) REVERT: F 80 TYR cc_start: 0.8771 (m-80) cc_final: 0.8409 (m-10) REVERT: F 135 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8361 (p) REVERT: L 98 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7404 (mttm) REVERT: G 21 ILE cc_start: 0.8409 (mm) cc_final: 0.8050 (mt) REVERT: G 46 GLN cc_start: 0.8243 (mt0) cc_final: 0.7753 (mp10) outliers start: 69 outliers final: 52 residues processed: 357 average time/residue: 0.1624 time to fit residues: 87.2030 Evaluate side-chains 349 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 215 optimal weight: 0.0040 chunk 216 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 226 optimal weight: 0.0670 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 219 optimal weight: 0.5980 chunk 241 optimal weight: 0.8980 overall best weight: 0.4930 ------------------------------------------------------------------------------- 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 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115888 restraints weight = 28283.466| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.38 r_work: 0.3208 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20073 Z= 0.139 Angle : 0.563 10.330 27309 Z= 0.300 Chirality : 0.042 0.167 2967 Planarity : 0.004 0.046 3519 Dihedral : 4.638 32.302 2733 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.30 % Allowed : 15.98 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.54 (0.17), residues: 2418 helix: -0.72 (0.26), residues: 342 sheet: -0.28 (0.18), residues: 810 loop : -0.15 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 43 TYR 0.022 0.001 TYR A 649 PHE 0.022 0.001 PHE C 650 TRP 0.013 0.001 TRP F 68 HIS 0.013 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00312 (20052) covalent geometry : angle 0.55957 (27267) SS BOND : bond 0.00353 ( 21) SS BOND : angle 1.70954 ( 42) hydrogen bonds : bond 0.03534 ( 761) hydrogen bonds : angle 5.71852 ( 2325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 326 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7369 (tp30) REVERT: A 233 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8209 (mm-30) REVERT: A 520 MET cc_start: 0.7809 (mmp) cc_final: 0.6822 (mmt) REVERT: A 536 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7694 (tt) REVERT: A 562 ARG cc_start: 0.7833 (ttt90) cc_final: 0.6980 (ttp80) REVERT: A 638 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7166 (mtp-110) REVERT: D 80 TYR cc_start: 0.8922 (m-80) cc_final: 0.8679 (m-80) REVERT: B 140 GLN cc_start: 0.6724 (tt0) cc_final: 0.6292 (tt0) REVERT: B 375 MET cc_start: 0.8472 (ttt) cc_final: 0.8215 (ttt) REVERT: B 562 ARG cc_start: 0.6391 (ptt90) cc_final: 0.6072 (ptt90) REVERT: B 587 MET cc_start: 0.7256 (mmm) cc_final: 0.6440 (mmm) REVERT: C 112 ASN cc_start: 0.7363 (t0) cc_final: 0.6860 (t0) REVERT: C 208 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.7827 (mtp85) REVERT: C 562 ARG cc_start: 0.8095 (ptt-90) cc_final: 0.7506 (ttp80) REVERT: C 709 ASN cc_start: 0.8676 (m-40) cc_final: 0.8439 (m110) REVERT: H 130 TYR cc_start: 0.8747 (m-80) cc_final: 0.8538 (m-10) REVERT: H 135 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8677 (p) REVERT: F 43 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: F 78 LYS cc_start: 0.8922 (mttt) cc_final: 0.8568 (mttt) REVERT: L 98 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7517 (mttm) REVERT: G 21 ILE cc_start: 0.8304 (mm) cc_final: 0.7929 (mt) REVERT: G 46 GLN cc_start: 0.8149 (mt0) cc_final: 0.7775 (mp10) REVERT: G 101 ARG cc_start: 0.7746 (mtm180) cc_final: 0.6643 (mmm-85) outliers start: 49 outliers final: 34 residues processed: 351 average time/residue: 0.1456 time to fit residues: 77.5853 Evaluate side-chains 346 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 233 optimal weight: 0.3980 chunk 81 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 65 optimal weight: 0.0040 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- 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 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114521 restraints weight = 28336.231| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.33 r_work: 0.3182 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20073 Z= 0.219 Angle : 0.597 10.217 27309 Z= 0.317 Chirality : 0.043 0.199 2967 Planarity : 0.005 0.045 3519 Dihedral : 4.706 30.138 2733 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.54 % Allowed : 16.36 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.52 (0.17), residues: 2418 helix: -0.50 (0.27), residues: 324 sheet: -0.34 (0.18), residues: 810 loop : -0.16 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.032 0.002 TYR B 689 PHE 0.018 0.002 PHE C 650 TRP 0.013 0.001 TRP F 68 HIS 0.013 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00504 (20052) covalent geometry : angle 0.59128 (27267) SS BOND : bond 0.00330 ( 21) SS BOND : angle 2.26600 ( 42) hydrogen bonds : bond 0.03715 ( 761) hydrogen bonds : angle 5.76345 ( 2325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7973 (m-80) cc_final: 0.7757 (m-80) REVERT: A 520 MET cc_start: 0.7830 (mmp) cc_final: 0.6844 (mmt) REVERT: A 536 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7681 (tt) REVERT: A 562 ARG cc_start: 0.7892 (ttt90) cc_final: 0.6993 (ttp80) REVERT: A 638 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.7277 (mtp-110) REVERT: D 80 TYR cc_start: 0.8913 (m-80) cc_final: 0.8677 (m-80) REVERT: D 110 ASP cc_start: 0.7022 (m-30) cc_final: 0.6040 (m-30) REVERT: B 140 GLN cc_start: 0.6753 (tt0) cc_final: 0.6357 (tt0) REVERT: B 375 MET cc_start: 0.8568 (ttt) cc_final: 0.8274 (ttt) REVERT: B 562 ARG cc_start: 0.6498 (ptt90) cc_final: 0.6253 (ptt90) REVERT: B 587 MET cc_start: 0.7300 (mmm) cc_final: 0.6463 (mmm) REVERT: C 112 ASN cc_start: 0.7379 (t0) cc_final: 0.6880 (t0) REVERT: C 195 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: C 208 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.7878 (mtp85) REVERT: C 413 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 562 ARG cc_start: 0.8116 (ptt-90) cc_final: 0.7506 (ttp80) REVERT: C 709 ASN cc_start: 0.8703 (m-40) cc_final: 0.8488 (m110) REVERT: H 135 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8687 (p) REVERT: F 43 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6461 (m-80) REVERT: F 78 LYS cc_start: 0.8919 (mttt) cc_final: 0.8532 (mttt) REVERT: F 80 TYR cc_start: 0.8734 (m-80) cc_final: 0.8342 (m-10) REVERT: L 98 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7510 (mttm) REVERT: G 21 ILE cc_start: 0.8396 (mm) cc_final: 0.8066 (mt) REVERT: G 46 GLN cc_start: 0.8131 (mt0) cc_final: 0.7727 (mp10) REVERT: G 101 ARG cc_start: 0.7773 (mtm180) cc_final: 0.6671 (mmm-85) outliers start: 54 outliers final: 44 residues processed: 338 average time/residue: 0.1518 time to fit residues: 77.0485 Evaluate side-chains 350 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 300 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113668 restraints weight = 28193.361| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.27 r_work: 0.3170 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20073 Z= 0.224 Angle : 0.606 9.898 27309 Z= 0.321 Chirality : 0.044 0.197 2967 Planarity : 0.005 0.045 3519 Dihedral : 4.736 26.099 2733 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.63 % Allowed : 16.46 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.62 (0.17), residues: 2418 helix: -0.72 (0.26), residues: 342 sheet: -0.34 (0.18), residues: 843 loop : -0.22 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.027 0.002 TYR B 689 PHE 0.019 0.002 PHE C 650 TRP 0.017 0.001 TRP F 68 HIS 0.013 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00513 (20052) covalent geometry : angle 0.60160 (27267) SS BOND : bond 0.00390 ( 21) SS BOND : angle 1.99638 ( 42) hydrogen bonds : bond 0.03758 ( 761) hydrogen bonds : angle 5.77556 ( 2325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7341 (tp30) REVERT: A 262 PHE cc_start: 0.7979 (m-80) cc_final: 0.7766 (m-80) REVERT: A 520 MET cc_start: 0.7816 (mmp) cc_final: 0.6815 (mmt) REVERT: A 536 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 562 ARG cc_start: 0.7887 (ttt90) cc_final: 0.6971 (ttp80) REVERT: A 638 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7388 (mtp-110) REVERT: D 80 TYR cc_start: 0.8942 (m-80) cc_final: 0.8648 (m-80) REVERT: B 140 GLN cc_start: 0.6735 (tt0) cc_final: 0.6341 (tt0) REVERT: B 375 MET cc_start: 0.8549 (ttt) cc_final: 0.8277 (ttt) REVERT: B 562 ARG cc_start: 0.6525 (ptt90) cc_final: 0.6267 (ptt90) REVERT: B 587 MET cc_start: 0.7338 (mmm) cc_final: 0.6450 (mmm) REVERT: C 112 ASN cc_start: 0.7383 (t0) cc_final: 0.6895 (t0) REVERT: C 195 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: C 208 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.7907 (mtp85) REVERT: C 413 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8036 (mp) REVERT: C 562 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7520 (ttp80) REVERT: C 709 ASN cc_start: 0.8736 (m-40) cc_final: 0.8492 (m110) REVERT: H 135 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8736 (p) REVERT: F 43 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: F 78 LYS cc_start: 0.8922 (mttt) cc_final: 0.8553 (mttt) REVERT: F 80 TYR cc_start: 0.8728 (m-80) cc_final: 0.8375 (m-10) REVERT: L 98 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7510 (mttm) REVERT: G 21 ILE cc_start: 0.8414 (mm) cc_final: 0.8113 (mt) REVERT: G 46 GLN cc_start: 0.8142 (mt0) cc_final: 0.7747 (mp10) REVERT: G 101 ARG cc_start: 0.7769 (mtm180) cc_final: 0.6680 (mmm-85) outliers start: 56 outliers final: 44 residues processed: 333 average time/residue: 0.1559 time to fit residues: 78.0420 Evaluate side-chains 344 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 207 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN B 129 GLN B 238 ASN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115639 restraints weight = 28282.734| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20073 Z= 0.156 Angle : 0.589 15.373 27309 Z= 0.310 Chirality : 0.042 0.181 2967 Planarity : 0.004 0.048 3519 Dihedral : 4.615 23.882 2733 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.54 % Allowed : 16.93 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.49 (0.17), residues: 2418 helix: -0.47 (0.27), residues: 324 sheet: -0.31 (0.18), residues: 825 loop : -0.14 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.030 0.001 TYR B 689 PHE 0.022 0.002 PHE C 650 TRP 0.016 0.001 TRP F 68 HIS 0.014 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00356 (20052) covalent geometry : angle 0.58565 (27267) SS BOND : bond 0.00296 ( 21) SS BOND : angle 1.78869 ( 42) hydrogen bonds : bond 0.03546 ( 761) hydrogen bonds : angle 5.67633 ( 2325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7365 (tp30) REVERT: A 262 PHE cc_start: 0.7922 (m-80) cc_final: 0.7716 (m-80) REVERT: A 428 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.7693 (ttt90) REVERT: A 520 MET cc_start: 0.7826 (mmp) cc_final: 0.6661 (mmt) REVERT: A 536 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7725 (tt) REVERT: A 562 ARG cc_start: 0.7864 (ttt90) cc_final: 0.6938 (ttp80) REVERT: A 638 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7361 (mtp-110) REVERT: D 80 TYR cc_start: 0.8898 (m-80) cc_final: 0.8579 (m-80) REVERT: B 140 GLN cc_start: 0.6730 (tt0) cc_final: 0.6327 (tt0) REVERT: B 375 MET cc_start: 0.8437 (ttt) cc_final: 0.8200 (ttt) REVERT: B 562 ARG cc_start: 0.6519 (ptt90) cc_final: 0.6252 (ptt90) REVERT: B 587 MET cc_start: 0.7311 (mmm) cc_final: 0.6431 (mmm) REVERT: B 622 GLU cc_start: 0.7209 (tt0) cc_final: 0.6607 (tt0) REVERT: C 112 ASN cc_start: 0.7334 (t0) cc_final: 0.6849 (t0) REVERT: C 195 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: C 208 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.7838 (mtp85) REVERT: C 413 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7994 (mp) REVERT: C 535 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7495 (mm-30) REVERT: C 562 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7434 (ttp80) REVERT: C 709 ASN cc_start: 0.8705 (m-40) cc_final: 0.8454 (m110) REVERT: C 714 LEU cc_start: 0.8238 (mt) cc_final: 0.8030 (mt) REVERT: H 32 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7772 (mmmt) REVERT: H 135 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8706 (p) REVERT: F 43 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: F 78 LYS cc_start: 0.8924 (mttt) cc_final: 0.8547 (mttt) REVERT: F 80 TYR cc_start: 0.8646 (m-80) cc_final: 0.8312 (m-10) REVERT: L 94 ASP cc_start: 0.7296 (p0) cc_final: 0.7072 (p0) REVERT: L 98 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7557 (mttm) REVERT: G 21 ILE cc_start: 0.8374 (mm) cc_final: 0.8049 (mt) REVERT: G 46 GLN cc_start: 0.8117 (mt0) cc_final: 0.7619 (mp10) REVERT: G 101 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6669 (mmm-85) outliers start: 54 outliers final: 46 residues processed: 339 average time/residue: 0.1692 time to fit residues: 85.1214 Evaluate side-chains 355 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 115 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 232 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN B 129 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN C 534 HIS ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115582 restraints weight = 28250.818| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.28 r_work: 0.3201 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20073 Z= 0.170 Angle : 0.592 15.060 27309 Z= 0.312 Chirality : 0.043 0.334 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.597 23.380 2733 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.68 % Allowed : 16.60 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: -0.47 (0.17), residues: 2418 helix: -0.48 (0.27), residues: 324 sheet: -0.29 (0.18), residues: 825 loop : -0.14 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.027 0.001 TYR A 649 PHE 0.028 0.002 PHE A 300 TRP 0.016 0.001 TRP F 68 HIS 0.015 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00392 (20052) covalent geometry : angle 0.58905 (27267) SS BOND : bond 0.00352 ( 21) SS BOND : angle 1.72382 ( 42) hydrogen bonds : bond 0.03582 ( 761) hydrogen bonds : angle 5.65027 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6561.66 seconds wall clock time: 112 minutes 39.90 seconds (6759.90 seconds total)