Starting phenix.real_space_refine on Tue May 20 07:56:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgz_19163/05_2025/8rgz_19163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgz_19163/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rgz_19163/05_2025/8rgz_19163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgz_19163/05_2025/8rgz_19163.map" model { file = "/net/cci-nas-00/data/ceres_data/8rgz_19163/05_2025/8rgz_19163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgz_19163/05_2025/8rgz_19163.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.37, per 1000 atoms: 0.58 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: 4.85 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.56 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: 8.36 Time building geometry restraints manager: 5.65 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: 0.01 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 46.460 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.500 ------------------------------------------------------------------------------- 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 : 12.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.088 0.016 TRP B 528 HIS 0.035 0.006 HIS B 712 PHE 0.066 0.010 PHE B 300 TYR 0.061 0.010 TYR C 157 ARG 0.049 0.003 ARG B 505 Details of bonding type rmsd hydrogen bonds : bond 0.13583 ( 761) hydrogen bonds : angle 7.77606 ( 2325) SS BOND : bond 0.04623 ( 21) SS BOND : angle 2.47811 ( 42) covalent geometry : bond 0.01057 (20052) covalent geometry : angle 1.09613 (27267) *********************** 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 : 2.236 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: 0.7002 (mtm110) REVERT: A 649 TYR cc_start: 0.7400 (t80) cc_final: 0.6855 (t80) REVERT: D 43 PHE cc_start: 0.8317 (m-10) cc_final: 0.7930 (m-10) REVERT: D 97 ASN cc_start: 0.6797 (t0) cc_final: 0.6265 (t0) 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: 0.8195 (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: 0.8141 (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: 0.6074 (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: 0.7957 (t60) REVERT: H 80 TYR cc_start: 0.8173 (m-80) cc_final: 0.7922 (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: 0.8038 (m-80) REVERT: G 23 MET cc_start: 0.7428 (mmm) cc_final: 0.7228 (mmm) 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: 0.3423 time to fit residues: 207.2251 Evaluate side-chains 326 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 205 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 220 optimal weight: 0.0060 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 255 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 217 ASN ** C 270 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116827 restraints weight = 28026.736| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.34 r_work: 0.3222 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 20073 Z= 0.182 Angle : 0.599 15.975 27309 Z= 0.319 Chirality : 0.043 0.154 2967 Planarity : 0.005 0.057 3519 Dihedral : 4.787 59.854 2738 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.46 % Allowed : 8.79 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2418 helix: -0.42 (0.27), residues: 324 sheet: -0.13 (0.17), residues: 903 loop : 0.11 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 354 HIS 0.013 0.001 HIS C 534 PHE 0.015 0.002 PHE B 650 TYR 0.015 0.002 TYR B 213 ARG 0.009 0.001 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 761) hydrogen bonds : angle 6.13107 ( 2325) SS BOND : bond 0.00421 ( 21) SS BOND : angle 2.85655 ( 42) covalent geometry : bond 0.00411 (20052) covalent geometry : angle 0.58843 (27267) *********************** 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 383 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 352 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.7746 (mmp) cc_final: 0.6970 (mmt) REVERT: A 562 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7481 (mtm110) REVERT: A 638 ARG cc_start: 0.7267 (mtp-110) cc_final: 0.6684 (mtm110) REVERT: A 649 TYR cc_start: 0.6779 (t80) cc_final: 0.5918 (t80) REVERT: D 110 ASP cc_start: 0.6526 (m-30) cc_final: 0.5617 (m-30) REVERT: B 140 GLN cc_start: 0.6665 (tt0) cc_final: 0.6245 (tt0) REVERT: B 374 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6762 (tm-30) REVERT: B 562 ARG cc_start: 0.6719 (ptt90) cc_final: 0.6335 (ptt90) REVERT: B 587 MET cc_start: 0.7150 (mmm) cc_final: 0.6676 (mmm) REVERT: B 678 LEU cc_start: 0.8743 (tp) cc_final: 0.8528 (tp) REVERT: C 112 ASN cc_start: 0.7247 (t0) cc_final: 0.6679 (t0) REVERT: C 385 ARG cc_start: 0.8352 (mpt180) cc_final: 0.7740 (mtp85) REVERT: C 562 ARG cc_start: 0.7666 (ptt-90) cc_final: 0.7234 (ttp80) REVERT: H 130 TYR cc_start: 0.8831 (m-80) cc_final: 0.8548 (m-10) REVERT: F 59 ARG cc_start: 0.7880 (ptt180) cc_final: 0.7536 (ptm-80) REVERT: F 64 LYS cc_start: 0.8315 (mptt) cc_final: 0.7413 (tmmt) REVERT: F 68 TRP cc_start: 0.8141 (t60) cc_final: 0.7847 (t60) REVERT: F 78 LYS cc_start: 0.8897 (mttt) cc_final: 0.8400 (mttt) REVERT: F 110 ASP cc_start: 0.7787 (m-30) cc_final: 0.7521 (m-30) REVERT: L 98 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7354 (mttm) REVERT: G 46 GLN cc_start: 0.7875 (mt0) cc_final: 0.7597 (mp10) outliers start: 31 outliers final: 21 residues processed: 369 average time/residue: 0.3351 time to fit residues: 184.3167 Evaluate side-chains 340 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 2.460 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** G 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112904 restraints weight = 28354.027| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.39 r_work: 0.3160 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 20073 Z= 0.290 Angle : 0.639 12.387 27309 Z= 0.340 Chirality : 0.046 0.170 2967 Planarity : 0.005 0.057 3519 Dihedral : 4.801 21.707 2733 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.21 % Allowed : 12.08 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2418 helix: -0.49 (0.26), residues: 324 sheet: -0.21 (0.17), residues: 885 loop : -0.00 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 528 HIS 0.014 0.002 HIS B 177 PHE 0.020 0.002 PHE A 159 TYR 0.019 0.002 TYR B 689 ARG 0.005 0.001 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 761) hydrogen bonds : angle 5.98653 ( 2325) SS BOND : bond 0.00874 ( 21) SS BOND : angle 2.61655 ( 42) covalent geometry : bond 0.00662 (20052) covalent geometry : angle 0.63130 (27267) *********************** 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 365 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 718 ASP cc_start: 0.8543 (t70) cc_final: 0.8316 (t70) REVERT: D 43 PHE cc_start: 0.7765 (m-10) cc_final: 0.7468 (m-10) REVERT: B 140 GLN cc_start: 0.6816 (tt0) cc_final: 0.6353 (tt0) REVERT: B 317 ASP cc_start: 0.8624 (p0) cc_final: 0.8312 (m-30) REVERT: B 374 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6912 (tm-30) REVERT: B 562 ARG cc_start: 0.6611 (ptt90) cc_final: 0.6334 (ptt90) REVERT: B 587 MET cc_start: 0.7272 (mmm) cc_final: 0.6696 (mmm) REVERT: B 622 GLU cc_start: 0.7259 (tt0) cc_final: 0.6857 (tt0) REVERT: C 112 ASN cc_start: 0.7245 (t0) cc_final: 0.6697 (t0) REVERT: C 562 ARG cc_start: 0.7784 (ptt-90) cc_final: 0.7229 (ttp80) REVERT: C 709 ASN cc_start: 0.8679 (m-40) cc_final: 0.8456 (m110) REVERT: F 43 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: F 64 LYS cc_start: 0.8397 (mptt) cc_final: 0.7499 (tmtt) REVERT: F 78 LYS cc_start: 0.8891 (mttt) cc_final: 0.8478 (mttt) REVERT: L 98 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7507 (mttm) REVERT: G 46 GLN cc_start: 0.8133 (mt0) cc_final: 0.7704 (mp10) outliers start: 47 outliers final: 31 residues processed: 343 average time/residue: 0.3295 time to fit residues: 169.5931 Evaluate side-chains 337 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 304 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 563 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain D residue 42 THR 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 B residue 720 ASP 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 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 194 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN C 321 GLN C 534 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116310 restraints weight = 28246.610| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.37 r_work: 0.3212 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20073 Z= 0.149 Angle : 0.555 10.559 27309 Z= 0.296 Chirality : 0.042 0.159 2967 Planarity : 0.005 0.053 3519 Dihedral : 4.601 25.023 2733 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 13.31 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2418 helix: -0.46 (0.26), residues: 330 sheet: -0.13 (0.18), residues: 855 loop : 0.04 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 354 HIS 0.010 0.001 HIS C 534 PHE 0.028 0.002 PHE A 641 TYR 0.024 0.001 TYR B 689 ARG 0.008 0.000 ARG L 101 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 761) hydrogen bonds : angle 5.71953 ( 2325) SS BOND : bond 0.00492 ( 21) SS BOND : angle 2.58942 ( 42) covalent geometry : bond 0.00332 (20052) covalent geometry : angle 0.54604 (27267) *********************** 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 381 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 331 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.7737 (mmp) cc_final: 0.6572 (mmt) REVERT: A 536 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 562 ARG cc_start: 0.8036 (ttt180) cc_final: 0.7621 (ptm160) REVERT: A 638 ARG cc_start: 0.7311 (mtp-110) cc_final: 0.7052 (mtp-110) REVERT: E 124 GLN cc_start: 0.8031 (mp10) cc_final: 0.7657 (mp10) REVERT: B 140 GLN cc_start: 0.6781 (tt0) cc_final: 0.6272 (tt0) REVERT: B 317 ASP cc_start: 0.8638 (p0) cc_final: 0.8258 (m-30) REVERT: B 374 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6857 (tm-30) REVERT: B 562 ARG cc_start: 0.6513 (ptt90) cc_final: 0.6195 (ptt90) REVERT: B 587 MET cc_start: 0.7204 (mmm) cc_final: 0.6491 (mmm) REVERT: B 622 GLU cc_start: 0.7122 (tt0) cc_final: 0.6678 (tt0) REVERT: C 112 ASN cc_start: 0.7251 (t0) cc_final: 0.6726 (t0) REVERT: C 208 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.7815 (mtp85) REVERT: C 562 ARG cc_start: 0.7788 (ptt-90) cc_final: 0.7215 (ttp80) REVERT: C 709 ASN cc_start: 0.8685 (m-40) cc_final: 0.8447 (m110) REVERT: C 714 LEU cc_start: 0.8255 (mt) cc_final: 0.8001 (mt) REVERT: H 128 MET cc_start: 0.8942 (mtm) cc_final: 0.8671 (mtm) REVERT: H 130 TYR cc_start: 0.8767 (m-80) cc_final: 0.8526 (m-10) REVERT: F 78 LYS cc_start: 0.8912 (mttt) cc_final: 0.8519 (mttt) REVERT: L 98 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7470 (mttm) REVERT: G 46 GLN cc_start: 0.8100 (mt0) cc_final: 0.7707 (mp10) REVERT: G 101 ARG cc_start: 0.7721 (mtm180) cc_final: 0.6656 (mmm-85) outliers start: 50 outliers final: 28 residues processed: 357 average time/residue: 0.3567 time to fit residues: 192.0434 Evaluate side-chains 329 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 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 A residue 676 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 42 THR 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 232 MET Chi-restraints excluded: chain B residue 241 THR 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 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 151 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 138 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 173 optimal weight: 0.0870 chunk 200 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3847 r_free = 0.3847 target = 0.147054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117715 restraints weight = 28288.072| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.38 r_work: 0.3227 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20073 Z= 0.135 Angle : 0.537 8.650 27309 Z= 0.286 Chirality : 0.042 0.202 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.483 22.719 2733 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.16 % Allowed : 14.29 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2418 helix: -0.34 (0.26), residues: 330 sheet: -0.07 (0.18), residues: 849 loop : 0.16 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 354 HIS 0.008 0.001 HIS B 534 PHE 0.018 0.001 PHE A 650 TYR 0.021 0.001 TYR A 649 ARG 0.005 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 761) hydrogen bonds : angle 5.56378 ( 2325) SS BOND : bond 0.00563 ( 21) SS BOND : angle 1.76662 ( 42) covalent geometry : bond 0.00305 (20052) covalent geometry : angle 0.53336 (27267) *********************** 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 371 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8214 (mp0) REVERT: A 520 MET cc_start: 0.7708 (mmp) cc_final: 0.6584 (mmt) REVERT: A 562 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7547 (ptm160) REVERT: A 638 ARG cc_start: 0.7512 (mtp-110) cc_final: 0.7209 (mtp-110) REVERT: A 677 MET cc_start: 0.8496 (mmt) cc_final: 0.8213 (mmp) REVERT: D 80 TYR cc_start: 0.8806 (m-80) cc_final: 0.8505 (m-80) REVERT: B 140 GLN cc_start: 0.6646 (tt0) cc_final: 0.6166 (tt0) REVERT: B 285 ASP cc_start: 0.8263 (p0) cc_final: 0.8059 (p0) REVERT: B 317 ASP cc_start: 0.8632 (p0) cc_final: 0.8215 (m-30) REVERT: B 374 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6793 (tm-30) REVERT: B 375 MET cc_start: 0.8493 (ttt) cc_final: 0.8257 (ttt) REVERT: B 562 ARG cc_start: 0.6553 (ptt90) cc_final: 0.6181 (ptt90) REVERT: B 587 MET cc_start: 0.7195 (mmm) cc_final: 0.6446 (mmm) REVERT: B 622 GLU cc_start: 0.7099 (tt0) cc_final: 0.6625 (tt0) REVERT: C 112 ASN cc_start: 0.7356 (t0) cc_final: 0.6850 (t0) REVERT: C 195 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: C 208 ARG cc_start: 0.8350 (mtt-85) cc_final: 0.7832 (mtp85) REVERT: C 562 ARG cc_start: 0.7903 (ptt-90) cc_final: 0.7319 (ttp80) REVERT: C 709 ASN cc_start: 0.8633 (m-40) cc_final: 0.8390 (m110) REVERT: C 714 LEU cc_start: 0.8258 (mt) cc_final: 0.8019 (mt) REVERT: H 24 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8294 (ttpp) REVERT: H 128 MET cc_start: 0.8910 (mtm) cc_final: 0.8664 (mtm) REVERT: H 135 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8701 (p) REVERT: F 43 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: F 78 LYS cc_start: 0.8914 (mttt) cc_final: 0.8505 (mttt) REVERT: L 98 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7449 (mttm) REVERT: G 21 ILE cc_start: 0.8218 (mm) cc_final: 0.7767 (mt) REVERT: G 46 GLN cc_start: 0.8122 (mt0) cc_final: 0.7761 (mp10) REVERT: G 101 ARG cc_start: 0.7719 (mtm180) cc_final: 0.6642 (mmm-85) outliers start: 46 outliers final: 26 residues processed: 349 average time/residue: 0.3404 time to fit residues: 180.2766 Evaluate side-chains 333 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 563 MET 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 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 243 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 534 HIS 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 84 LEU Chi-restraints excluded: chain H residue 135 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN C 458 ASN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 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 = 0.3846 r_free = 0.3846 target = 0.146834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117529 restraints weight = 28218.593| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.38 r_work: 0.3222 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20073 Z= 0.153 Angle : 0.543 8.800 27309 Z= 0.290 Chirality : 0.042 0.218 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.501 30.740 2733 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 14.81 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2418 helix: -0.43 (0.26), residues: 324 sheet: -0.07 (0.18), residues: 849 loop : 0.12 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 354 HIS 0.008 0.001 HIS B 534 PHE 0.018 0.001 PHE A 650 TYR 0.025 0.001 TYR B 689 ARG 0.006 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 761) hydrogen bonds : angle 5.54148 ( 2325) SS BOND : bond 0.00355 ( 21) SS BOND : angle 1.79649 ( 42) covalent geometry : bond 0.00351 (20052) covalent geometry : angle 0.53850 (27267) *********************** 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 378 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7334 (tp30) REVERT: A 520 MET cc_start: 0.7721 (mmp) cc_final: 0.6584 (mmt) REVERT: A 536 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (tt) REVERT: A 562 ARG cc_start: 0.8015 (ttt180) cc_final: 0.7574 (ptm160) REVERT: A 638 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7185 (mtp-110) REVERT: D 80 TYR cc_start: 0.8826 (m-80) cc_final: 0.8520 (m-80) REVERT: B 140 GLN cc_start: 0.6708 (tt0) cc_final: 0.6213 (tt0) REVERT: B 285 ASP cc_start: 0.8253 (p0) cc_final: 0.8020 (p0) REVERT: B 374 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6846 (tm-30) REVERT: B 375 MET cc_start: 0.8459 (ttt) cc_final: 0.8207 (ttt) REVERT: B 562 ARG cc_start: 0.6425 (ptt90) cc_final: 0.6163 (ptt90) REVERT: B 587 MET cc_start: 0.7290 (mmm) cc_final: 0.6555 (mmm) REVERT: C 112 ASN cc_start: 0.7360 (t0) cc_final: 0.6862 (t0) REVERT: C 195 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: C 208 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.7844 (mtp85) REVERT: C 562 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7315 (ttp80) REVERT: C 709 ASN cc_start: 0.8643 (m-40) cc_final: 0.8390 (m110) REVERT: C 714 LEU cc_start: 0.8246 (mt) cc_final: 0.8035 (mt) REVERT: H 32 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7622 (mmmt) REVERT: H 135 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8631 (p) REVERT: F 43 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: F 78 LYS cc_start: 0.8929 (mttt) cc_final: 0.8520 (mttt) REVERT: L 84 ASP cc_start: 0.7683 (t0) cc_final: 0.7396 (m-30) REVERT: L 98 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7511 (mttm) REVERT: G 21 ILE cc_start: 0.8263 (mm) cc_final: 0.7855 (mt) REVERT: G 46 GLN cc_start: 0.8150 (mt0) cc_final: 0.7819 (mp10) REVERT: G 101 ARG cc_start: 0.7727 (mtm180) cc_final: 0.6643 (mmm-85) outliers start: 53 outliers final: 34 residues processed: 355 average time/residue: 0.3289 time to fit residues: 175.9125 Evaluate side-chains 349 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 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 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 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 317 ASP Chi-restraints excluded: chain C residue 534 HIS 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 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 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 106 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116158 restraints weight = 28286.797| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.33 r_work: 0.3212 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20073 Z= 0.194 Angle : 0.572 12.361 27309 Z= 0.303 Chirality : 0.043 0.193 2967 Planarity : 0.004 0.046 3519 Dihedral : 4.555 26.287 2733 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.59 % Allowed : 15.37 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2418 helix: -0.41 (0.27), residues: 318 sheet: -0.04 (0.18), residues: 825 loop : 0.03 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 68 HIS 0.019 0.001 HIS C 516 PHE 0.016 0.002 PHE A 650 TYR 0.023 0.001 TYR A 649 ARG 0.007 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 761) hydrogen bonds : angle 5.58683 ( 2325) SS BOND : bond 0.00414 ( 21) SS BOND : angle 1.71671 ( 42) covalent geometry : bond 0.00446 (20052) covalent geometry : angle 0.56815 (27267) *********************** 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 377 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 322 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7282 (tp30) REVERT: A 233 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8184 (mm-30) REVERT: A 520 MET cc_start: 0.7738 (mmp) cc_final: 0.6697 (mmt) REVERT: A 536 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7620 (tt) REVERT: A 562 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7589 (ptm160) REVERT: A 638 ARG cc_start: 0.7586 (mtp-110) cc_final: 0.7210 (mtp-110) REVERT: A 718 ASP cc_start: 0.8164 (t0) cc_final: 0.7935 (t70) REVERT: D 25 GLU cc_start: 0.8740 (pm20) cc_final: 0.8493 (pm20) REVERT: D 80 TYR cc_start: 0.8835 (m-80) cc_final: 0.8487 (m-80) REVERT: B 140 GLN cc_start: 0.6683 (tt0) cc_final: 0.6211 (tt0) REVERT: B 285 ASP cc_start: 0.8272 (p0) cc_final: 0.8036 (p0) REVERT: B 375 MET cc_start: 0.8532 (ttt) cc_final: 0.8263 (ttt) REVERT: B 587 MET cc_start: 0.7298 (mmm) cc_final: 0.6534 (mmm) REVERT: B 622 GLU cc_start: 0.7120 (tt0) cc_final: 0.6654 (tt0) REVERT: C 112 ASN cc_start: 0.7353 (t0) cc_final: 0.6858 (t0) REVERT: C 195 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: C 208 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.7860 (mtp85) REVERT: C 421 MET cc_start: 0.7874 (mtt) cc_final: 0.7519 (tpp) REVERT: C 562 ARG cc_start: 0.7915 (ptt-90) cc_final: 0.7313 (ttp80) REVERT: C 709 ASN cc_start: 0.8678 (m-40) cc_final: 0.8451 (m110) REVERT: C 714 LEU cc_start: 0.8278 (mt) cc_final: 0.8048 (mt) REVERT: H 96 LYS cc_start: 0.8493 (mptt) cc_final: 0.8251 (mtmm) REVERT: F 43 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: F 78 LYS cc_start: 0.8933 (mttt) cc_final: 0.8522 (mttt) REVERT: F 80 TYR cc_start: 0.8646 (m-80) cc_final: 0.8277 (m-10) REVERT: F 106 MET cc_start: 0.7211 (mmm) cc_final: 0.6620 (mmm) REVERT: L 84 ASP cc_start: 0.7701 (t0) cc_final: 0.7410 (m-30) REVERT: L 98 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7516 (mttm) REVERT: L 101 ARG cc_start: 0.7766 (ttt90) cc_final: 0.7267 (tpt170) REVERT: G 21 ILE cc_start: 0.8305 (mm) cc_final: 0.7929 (mt) REVERT: G 46 GLN cc_start: 0.8140 (mt0) cc_final: 0.7755 (mp10) outliers start: 55 outliers final: 45 residues processed: 351 average time/residue: 0.3344 time to fit residues: 176.6164 Evaluate side-chains 356 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 2.296 ------------------------------------------------------------------------------- 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 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 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 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 347 THR 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 281 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 534 HIS 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 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 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 26 THR Chi-restraints excluded: chain L residue 98 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 236 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 211 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 238 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117708 restraints weight = 28313.925| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.34 r_work: 0.3232 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20073 Z= 0.142 Angle : 0.542 10.782 27309 Z= 0.288 Chirality : 0.042 0.178 2967 Planarity : 0.004 0.045 3519 Dihedral : 4.414 24.406 2733 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.16 % Allowed : 16.41 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2418 helix: -0.27 (0.27), residues: 327 sheet: 0.00 (0.18), residues: 840 loop : 0.08 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 68 HIS 0.014 0.001 HIS C 516 PHE 0.024 0.001 PHE A 300 TYR 0.028 0.001 TYR B 655 ARG 0.007 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 761) hydrogen bonds : angle 5.49135 ( 2325) SS BOND : bond 0.00361 ( 21) SS BOND : angle 1.71716 ( 42) covalent geometry : bond 0.00324 (20052) covalent geometry : angle 0.53850 (27267) *********************** 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 374 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7177 (tp30) REVERT: A 233 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 428 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.7723 (ttt180) REVERT: A 520 MET cc_start: 0.7743 (mmp) cc_final: 0.6759 (mmt) REVERT: A 536 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7462 (tt) REVERT: A 562 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7588 (ptm160) REVERT: A 638 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7379 (mtp-110) REVERT: A 718 ASP cc_start: 0.8192 (t0) cc_final: 0.7946 (t70) REVERT: D 80 TYR cc_start: 0.8803 (m-80) cc_final: 0.8497 (m-80) REVERT: E 129 GLU cc_start: 0.4802 (tp30) cc_final: 0.4479 (mt-10) REVERT: B 140 GLN cc_start: 0.6832 (tt0) cc_final: 0.6334 (tt0) REVERT: B 285 ASP cc_start: 0.8295 (p0) cc_final: 0.8050 (p0) REVERT: B 375 MET cc_start: 0.8268 (ttt) cc_final: 0.8034 (ttt) REVERT: B 587 MET cc_start: 0.7232 (mmm) cc_final: 0.6479 (mmm) REVERT: C 112 ASN cc_start: 0.7378 (t0) cc_final: 0.6881 (t0) REVERT: C 195 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: C 208 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7729 (mtp85) REVERT: C 562 ARG cc_start: 0.7904 (ptt-90) cc_final: 0.7330 (ttp80) REVERT: C 709 ASN cc_start: 0.8640 (m-40) cc_final: 0.8386 (m110) REVERT: C 714 LEU cc_start: 0.8197 (mt) cc_final: 0.7986 (mt) REVERT: H 96 LYS cc_start: 0.8477 (mptt) cc_final: 0.8247 (mtmm) REVERT: H 135 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8492 (p) REVERT: F 43 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: F 78 LYS cc_start: 0.8933 (mttt) cc_final: 0.8509 (mttt) REVERT: F 80 TYR cc_start: 0.8586 (m-80) cc_final: 0.8217 (m-10) REVERT: L 98 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7563 (mttm) REVERT: L 101 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7262 (tpt170) REVERT: G 46 GLN cc_start: 0.8119 (mt0) cc_final: 0.7783 (mp10) outliers start: 46 outliers final: 35 residues processed: 350 average time/residue: 0.3229 time to fit residues: 169.5399 Evaluate side-chains 346 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 94 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 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 347 THR 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 459 THR 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 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 136 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 175 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 211 optimal weight: 0.0870 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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 546 ASN C 512 HIS ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116734 restraints weight = 28163.386| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.30 r_work: 0.3221 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.004 0.062 20073 Z= 0.171 Angle : 0.569 10.247 27309 Z= 0.300 Chirality : 0.043 0.291 2967 Planarity : 0.004 0.045 3519 Dihedral : 4.495 27.497 2733 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.30 % Allowed : 16.50 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2418 helix: -0.30 (0.27), residues: 321 sheet: -0.01 (0.18), residues: 840 loop : 0.04 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 68 HIS 0.022 0.001 HIS C 516 PHE 0.022 0.002 PHE A 300 TYR 0.025 0.001 TYR A 649 ARG 0.008 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 761) hydrogen bonds : angle 5.53778 ( 2325) SS BOND : bond 0.00338 ( 21) SS BOND : angle 2.00871 ( 42) covalent geometry : bond 0.00392 (20052) covalent geometry : angle 0.56403 (27267) *********************** 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 354 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 520 MET cc_start: 0.7742 (mmp) cc_final: 0.6778 (mmt) REVERT: A 536 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7495 (tt) REVERT: A 562 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7628 (ptm160) REVERT: A 638 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7447 (mtp-110) REVERT: A 718 ASP cc_start: 0.8179 (t0) cc_final: 0.7915 (t70) REVERT: D 80 TYR cc_start: 0.8816 (m-80) cc_final: 0.8468 (m-80) REVERT: E 129 GLU cc_start: 0.5176 (tp30) cc_final: 0.4800 (mt-10) REVERT: B 140 GLN cc_start: 0.6798 (tt0) cc_final: 0.6336 (tt0) REVERT: B 285 ASP cc_start: 0.8271 (p0) cc_final: 0.8025 (p0) REVERT: B 375 MET cc_start: 0.8422 (ttt) cc_final: 0.8191 (ttt) REVERT: B 587 MET cc_start: 0.7250 (mmm) cc_final: 0.6410 (mmm) REVERT: C 112 ASN cc_start: 0.7335 (t0) cc_final: 0.6866 (t0) REVERT: C 195 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: C 208 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7746 (mtp85) REVERT: C 421 MET cc_start: 0.7921 (mtt) cc_final: 0.7579 (tpp) REVERT: C 562 ARG cc_start: 0.7937 (ptt-90) cc_final: 0.7367 (ttp80) REVERT: C 709 ASN cc_start: 0.8674 (m-40) cc_final: 0.8416 (m110) REVERT: C 714 LEU cc_start: 0.8243 (mt) cc_final: 0.8021 (mt) REVERT: H 96 LYS cc_start: 0.8499 (mptt) cc_final: 0.8263 (mtmm) REVERT: H 135 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8423 (p) REVERT: F 43 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6360 (m-80) REVERT: F 78 LYS cc_start: 0.8916 (mttt) cc_final: 0.8501 (mttt) REVERT: F 80 TYR cc_start: 0.8647 (m-80) cc_final: 0.8315 (m-10) REVERT: F 110 ASP cc_start: 0.7742 (m-30) cc_final: 0.7422 (m-30) REVERT: L 98 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7570 (mttm) REVERT: G 46 GLN cc_start: 0.8155 (mt0) cc_final: 0.7808 (mp10) outliers start: 49 outliers final: 44 residues processed: 330 average time/residue: 0.3307 time to fit residues: 164.8433 Evaluate side-chains 348 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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 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 676 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 128 MET 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 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 347 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 546 ASN 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 459 THR Chi-restraints excluded: chain C residue 534 HIS 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 H residue 136 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 72 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** D 35 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.147929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118307 restraints weight = 28135.095| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.30 r_work: 0.3246 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20073 Z= 0.134 Angle : 0.553 10.205 27309 Z= 0.292 Chirality : 0.042 0.303 2967 Planarity : 0.004 0.073 3519 Dihedral : 4.421 27.994 2733 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.12 % Allowed : 16.83 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2418 helix: -0.24 (0.27), residues: 327 sheet: 0.04 (0.18), residues: 840 loop : 0.04 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 68 HIS 0.018 0.001 HIS C 516 PHE 0.024 0.001 PHE A 300 TYR 0.028 0.001 TYR A 649 ARG 0.009 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 761) hydrogen bonds : angle 5.47042 ( 2325) SS BOND : bond 0.00357 ( 21) SS BOND : angle 1.63456 ( 42) covalent geometry : bond 0.00306 (20052) covalent geometry : angle 0.54928 (27267) ********************** 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 357 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 312 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7336 (tp30) REVERT: A 233 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8146 (mm-30) REVERT: A 520 MET cc_start: 0.7725 (mmp) cc_final: 0.6776 (mmt) REVERT: A 536 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7471 (tt) REVERT: A 562 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7623 (ptm160) REVERT: A 638 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7400 (mtp-110) REVERT: A 718 ASP cc_start: 0.8151 (t0) cc_final: 0.7904 (t70) REVERT: D 80 TYR cc_start: 0.8791 (m-80) cc_final: 0.8461 (m-80) REVERT: E 78 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7821 (ttp-110) REVERT: E 129 GLU cc_start: 0.5186 (tp30) cc_final: 0.4794 (mt-10) REVERT: B 140 GLN cc_start: 0.6796 (tt0) cc_final: 0.6335 (tt0) REVERT: B 285 ASP cc_start: 0.8266 (p0) cc_final: 0.8021 (p0) REVERT: B 375 MET cc_start: 0.8239 (ttt) cc_final: 0.8024 (ttt) REVERT: B 587 MET cc_start: 0.7259 (mmm) cc_final: 0.6426 (mmm) REVERT: C 112 ASN cc_start: 0.7327 (t0) cc_final: 0.6849 (t0) REVERT: C 195 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: C 208 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7727 (mtp85) REVERT: C 421 MET cc_start: 0.7881 (mtt) cc_final: 0.7509 (tpp) REVERT: C 562 ARG cc_start: 0.7924 (ptt-90) cc_final: 0.7347 (ttp80) REVERT: C 709 ASN cc_start: 0.8653 (m-40) cc_final: 0.8397 (m110) REVERT: C 714 LEU cc_start: 0.8228 (mt) cc_final: 0.8018 (mt) REVERT: H 135 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8413 (p) REVERT: F 43 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: F 78 LYS cc_start: 0.8919 (mttt) cc_final: 0.8514 (mttt) REVERT: F 80 TYR cc_start: 0.8554 (m-80) cc_final: 0.8208 (m-10) REVERT: L 72 ILE cc_start: 0.8602 (mm) cc_final: 0.8307 (mm) REVERT: L 98 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7570 (mttm) REVERT: G 46 GLN cc_start: 0.8133 (mt0) cc_final: 0.7660 (mp10) outliers start: 45 outliers final: 36 residues processed: 334 average time/residue: 0.3200 time to fit residues: 160.5071 Evaluate side-chains 345 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 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 676 THR Chi-restraints excluded: chain A residue 720 ASP 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 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 567 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR 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 84 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 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 L residue 26 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain G residue 94 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** E 124 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116764 restraints weight = 28342.773| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.33 r_work: 0.3220 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20073 Z= 0.181 Angle : 0.577 11.569 27309 Z= 0.304 Chirality : 0.043 0.291 2967 Planarity : 0.004 0.050 3519 Dihedral : 4.488 26.657 2733 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.30 % Allowed : 16.74 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2418 helix: -0.24 (0.27), residues: 321 sheet: -0.03 (0.18), residues: 840 loop : -0.03 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 68 HIS 0.019 0.001 HIS C 516 PHE 0.020 0.002 PHE A 300 TYR 0.027 0.001 TYR A 649 ARG 0.009 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 761) hydrogen bonds : angle 5.53300 ( 2325) SS BOND : bond 0.00317 ( 21) SS BOND : angle 1.60065 ( 42) covalent geometry : bond 0.00415 (20052) covalent geometry : angle 0.57422 (27267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12749.29 seconds wall clock time: 220 minutes 20.27 seconds (13220.27 seconds total)