Starting phenix.real_space_refine on Thu Jan 23 04:44:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgz_19163/01_2025/8rgz_19163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgz_19163/01_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_19163/01_2025/8rgz_19163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgz_19163/01_2025/8rgz_19163.map" model { file = "/net/cci-nas-00/data/ceres_data/8rgz_19163/01_2025/8rgz_19163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgz_19163/01_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 11.15, per 1000 atoms: 0.57 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: 4.60 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: 3.25 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: 8.51 Time building geometry restraints manager: 5.41 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: 2.180 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.830 Find NCS groups from input model: 0.620 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.650 ------------------------------------------------------------------------------- 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 0.114 20052 Z= 0.694 Angle : 1.096 8.259 27267 Z= 0.707 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 *********************** 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: 0.3526 time to fit residues: 213.2991 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 : 2.247 ------------------------------------------------------------------------------- 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: 4.9990 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 20052 Z= 0.267 Angle : 0.588 8.286 27267 Z= 0.314 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 *********************** 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 : 2.260 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: 0.3461 time to fit residues: 190.2142 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 : 2.190 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.143303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113680 restraints weight = 28294.701| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.31 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 20052 Z= 0.429 Angle : 0.628 10.021 27267 Z= 0.334 Chirality : 0.045 0.170 2967 Planarity : 0.005 0.056 3519 Dihedral : 4.775 22.438 2733 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 11.99 % Favored : 85.80 % 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: -0.31 (0.17), residues: 2418 helix: -0.48 (0.26), residues: 324 sheet: -0.15 (0.17), residues: 867 loop : 0.00 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 528 HIS 0.015 0.002 HIS B 177 PHE 0.020 0.002 PHE A 159 TYR 0.018 0.002 TYR B 689 ARG 0.005 0.001 ARG D 59 *********************** 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 366 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 319 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 718 ASP cc_start: 0.8524 (t70) cc_final: 0.8310 (t70) REVERT: B 140 GLN cc_start: 0.6789 (tt0) cc_final: 0.6350 (tt0) REVERT: B 317 ASP cc_start: 0.8589 (p0) cc_final: 0.8292 (m-30) REVERT: B 374 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6900 (tm-30) REVERT: B 562 ARG cc_start: 0.6615 (ptt90) cc_final: 0.6335 (ptt90) REVERT: B 587 MET cc_start: 0.7213 (mmm) cc_final: 0.6613 (mmm) REVERT: B 622 GLU cc_start: 0.7263 (tt0) cc_final: 0.6850 (tt0) REVERT: C 112 ASN cc_start: 0.7259 (t0) cc_final: 0.6728 (t0) REVERT: C 562 ARG cc_start: 0.7792 (ptt-90) cc_final: 0.7241 (ttp80) REVERT: C 709 ASN cc_start: 0.8659 (m-40) cc_final: 0.8437 (m110) REVERT: H 130 TYR cc_start: 0.8841 (m-80) cc_final: 0.8530 (m-10) REVERT: F 43 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: F 64 LYS cc_start: 0.8389 (mptt) cc_final: 0.7507 (tmtt) REVERT: F 78 LYS cc_start: 0.8888 (mttt) cc_final: 0.8438 (mttt) REVERT: L 98 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7507 (mttm) REVERT: G 46 GLN cc_start: 0.8137 (mt0) cc_final: 0.7726 (mp10) outliers start: 47 outliers final: 30 residues processed: 345 average time/residue: 0.3443 time to fit residues: 180.2270 Evaluate side-chains 332 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS 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 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 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 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 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: 2.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 chunk 159 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3834 r_free = 0.3834 target = 0.145983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116358 restraints weight = 28219.187| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.34 r_work: 0.3212 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20052 Z= 0.222 Angle : 0.544 10.943 27267 Z= 0.291 Chirality : 0.042 0.159 2967 Planarity : 0.005 0.053 3519 Dihedral : 4.574 25.035 2733 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.35 % Allowed : 13.21 % Favored : 84.44 % 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: -0.24 (0.17), residues: 2418 helix: -0.44 (0.26), residues: 330 sheet: -0.11 (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 0.011 0.001 HIS C 516 PHE 0.026 0.002 PHE A 641 TYR 0.022 0.001 TYR B 689 ARG 0.007 0.000 ARG L 101 *********************** 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 379 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.7742 (mmp) cc_final: 0.6581 (mmt) REVERT: A 536 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7558 (tt) REVERT: A 638 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.7035 (mtp-110) REVERT: A 677 MET cc_start: 0.8445 (mmt) cc_final: 0.8130 (mmp) REVERT: E 124 GLN cc_start: 0.7947 (mp10) cc_final: 0.7640 (mp10) REVERT: B 140 GLN cc_start: 0.6789 (tt0) cc_final: 0.6277 (tt0) REVERT: B 317 ASP cc_start: 0.8646 (p0) cc_final: 0.8266 (m-30) REVERT: B 374 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6840 (tm-30) REVERT: B 562 ARG cc_start: 0.6579 (ptt90) cc_final: 0.6346 (ptt90) REVERT: B 587 MET cc_start: 0.7223 (mmm) cc_final: 0.6527 (mmm) REVERT: B 622 GLU cc_start: 0.7137 (tt0) cc_final: 0.6695 (tt0) REVERT: C 112 ASN cc_start: 0.7267 (t0) cc_final: 0.6740 (t0) REVERT: C 208 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.7834 (mtp85) REVERT: C 562 ARG cc_start: 0.7786 (ptt-90) cc_final: 0.7222 (ttp80) REVERT: C 709 ASN cc_start: 0.8685 (m-40) cc_final: 0.8448 (m110) REVERT: C 714 LEU cc_start: 0.8299 (mt) cc_final: 0.8055 (mt) REVERT: H 128 MET cc_start: 0.8935 (mtm) cc_final: 0.8665 (mtm) REVERT: H 130 TYR cc_start: 0.8680 (m-80) cc_final: 0.8461 (m-10) REVERT: F 78 LYS cc_start: 0.8914 (mttt) cc_final: 0.8485 (mttt) REVERT: L 98 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7475 (mttm) REVERT: G 46 GLN cc_start: 0.8103 (mt0) cc_final: 0.7712 (mp10) REVERT: G 101 ARG cc_start: 0.7726 (mtm180) cc_final: 0.6661 (mmm-85) outliers start: 50 outliers final: 27 residues processed: 356 average time/residue: 0.3407 time to fit residues: 182.8285 Evaluate side-chains 333 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 304 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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 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 E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 297 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 151 optimal weight: 0.6980 chunk 204 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.144890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115315 restraints weight = 28437.901| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20052 Z= 0.283 Angle : 0.561 9.637 27267 Z= 0.299 Chirality : 0.043 0.215 2967 Planarity : 0.004 0.046 3519 Dihedral : 4.591 22.285 2733 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.59 % Allowed : 14.01 % Favored : 83.40 % 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: -0.18 (0.17), residues: 2418 helix: -0.40 (0.26), residues: 330 sheet: -0.13 (0.18), residues: 882 loop : 0.16 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.009 0.001 HIS B 534 PHE 0.020 0.002 PHE A 641 TYR 0.021 0.001 TYR A 164 ARG 0.005 0.000 ARG E 43 *********************** 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 378 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8148 (mp0) REVERT: A 520 MET cc_start: 0.7751 (mmp) cc_final: 0.6595 (mmt) REVERT: A 536 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 562 ARG cc_start: 0.7794 (ttt90) cc_final: 0.7461 (ptm160) REVERT: A 638 ARG cc_start: 0.7508 (mtp-110) cc_final: 0.7202 (mtp-110) REVERT: A 677 MET cc_start: 0.8481 (mmt) cc_final: 0.8217 (mmp) REVERT: B 140 GLN cc_start: 0.6666 (tt0) cc_final: 0.6211 (tt0) REVERT: B 374 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6888 (tm-30) REVERT: B 375 MET cc_start: 0.8518 (ttt) cc_final: 0.8271 (ttt) REVERT: B 562 ARG cc_start: 0.6588 (ptt90) cc_final: 0.6189 (ptt90) REVERT: B 587 MET cc_start: 0.7199 (mmm) cc_final: 0.6433 (mmm) REVERT: B 622 GLU cc_start: 0.7125 (tt0) cc_final: 0.6654 (tt0) REVERT: C 112 ASN cc_start: 0.7267 (t0) cc_final: 0.6740 (t0) REVERT: C 136 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7902 (mmm-85) REVERT: C 195 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: C 208 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.7847 (mtp85) REVERT: C 562 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7330 (ttp80) REVERT: C 709 ASN cc_start: 0.8686 (m-40) cc_final: 0.8472 (m110) REVERT: H 24 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8321 (ttpp) REVERT: H 25 GLU cc_start: 0.8235 (pm20) cc_final: 0.8000 (pm20) REVERT: H 128 MET cc_start: 0.8940 (mtm) cc_final: 0.8700 (mtm) REVERT: H 130 TYR cc_start: 0.8759 (m-80) cc_final: 0.8523 (m-10) REVERT: H 135 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (p) REVERT: F 43 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: F 78 LYS cc_start: 0.8915 (mttt) cc_final: 0.8520 (mttt) REVERT: L 98 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7450 (mttm) REVERT: G 21 ILE cc_start: 0.8269 (mm) cc_final: 0.7839 (mt) REVERT: G 46 GLN cc_start: 0.8154 (mt0) cc_final: 0.7743 (mp10) outliers start: 55 outliers final: 38 residues processed: 355 average time/residue: 0.3457 time to fit residues: 184.9149 Evaluate side-chains 341 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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 392 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 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 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 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: 2.9990 chunk 64 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3836 r_free = 0.3836 target = 0.146044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116754 restraints weight = 28241.599| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.36 r_work: 0.3220 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20052 Z= 0.232 Angle : 0.542 9.091 27267 Z= 0.289 Chirality : 0.042 0.167 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.506 21.437 2733 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 15.19 % Favored : 82.32 % 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: -0.37 (0.27), residues: 330 sheet: -0.15 (0.18), residues: 849 loop : 0.13 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 354 HIS 0.009 0.001 HIS B 534 PHE 0.022 0.002 PHE A 641 TYR 0.023 0.001 TYR A 164 ARG 0.007 0.000 ARG E 43 *********************** 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 379 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7256 (tp30) REVERT: A 520 MET cc_start: 0.7732 (mmp) cc_final: 0.6572 (mmt) REVERT: A 536 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7563 (tt) REVERT: A 562 ARG cc_start: 0.7796 (ttt90) cc_final: 0.7458 (ptm160) REVERT: A 638 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7174 (mtp-110) REVERT: A 677 MET cc_start: 0.8476 (mmt) cc_final: 0.8225 (mmp) REVERT: E 129 GLU cc_start: 0.4748 (tp30) cc_final: 0.4446 (mt-10) REVERT: B 140 GLN cc_start: 0.6696 (tt0) cc_final: 0.6213 (tt0) REVERT: B 374 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6843 (tm-30) REVERT: B 375 MET cc_start: 0.8470 (ttt) cc_final: 0.8210 (ttt) REVERT: B 562 ARG cc_start: 0.6406 (ptt90) cc_final: 0.6078 (ptt90) REVERT: B 587 MET cc_start: 0.7272 (mmm) cc_final: 0.6538 (mmm) REVERT: C 112 ASN cc_start: 0.7347 (t0) cc_final: 0.6847 (t0) REVERT: C 195 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: C 208 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.7837 (mtp85) REVERT: C 562 ARG cc_start: 0.7910 (ptt-90) cc_final: 0.7316 (ttp80) REVERT: C 709 ASN cc_start: 0.8661 (m-40) cc_final: 0.8414 (m110) REVERT: C 714 LEU cc_start: 0.8237 (mt) cc_final: 0.8009 (mt) REVERT: H 24 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8314 (ttpp) REVERT: H 32 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7654 (mmmt) REVERT: H 128 MET cc_start: 0.8921 (mtm) cc_final: 0.8653 (mtm) REVERT: H 135 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8776 (p) REVERT: F 43 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: F 78 LYS cc_start: 0.8921 (mttt) cc_final: 0.8507 (mttt) REVERT: F 80 TYR cc_start: 0.8566 (m-80) cc_final: 0.8190 (m-10) REVERT: L 98 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7516 (mttm) REVERT: G 21 ILE cc_start: 0.8278 (mm) cc_final: 0.7867 (mt) REVERT: G 46 GLN cc_start: 0.8132 (mt0) cc_final: 0.7731 (mp10) REVERT: G 101 ARG cc_start: 0.7732 (mtm180) cc_final: 0.6664 (mmm-85) outliers start: 53 outliers final: 36 residues processed: 352 average time/residue: 0.3373 time to fit residues: 178.3773 Evaluate side-chains 347 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 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 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 297 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 106 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN C 458 ASN ** 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 = 0.3801 r_free = 0.3801 target = 0.143190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113583 restraints weight = 28487.867| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.39 r_work: 0.3167 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20052 Z= 0.386 Angle : 0.607 12.033 27267 Z= 0.322 Chirality : 0.044 0.222 2967 Planarity : 0.005 0.045 3519 Dihedral : 4.728 30.374 2733 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.06 % Allowed : 15.47 % Favored : 81.48 % 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: -0.53 (0.17), residues: 2418 helix: -0.83 (0.26), residues: 336 sheet: -0.24 (0.18), residues: 825 loop : -0.14 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 68 HIS 0.009 0.002 HIS B 534 PHE 0.022 0.002 PHE A 641 TYR 0.028 0.002 TYR B 689 ARG 0.007 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8284 (mm-30) REVERT: A 520 MET cc_start: 0.7783 (mmp) cc_final: 0.7417 (mmm) REVERT: A 536 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7714 (tt) REVERT: A 562 ARG cc_start: 0.7881 (ttt90) cc_final: 0.7037 (ttp80) REVERT: A 677 MET cc_start: 0.8467 (mmt) cc_final: 0.8232 (mmp) REVERT: D 80 TYR cc_start: 0.8946 (m-80) cc_final: 0.8450 (m-80) REVERT: B 140 GLN cc_start: 0.6763 (tt0) cc_final: 0.6315 (tt0) REVERT: B 375 MET cc_start: 0.8603 (ttt) cc_final: 0.8327 (ttt) REVERT: B 562 ARG cc_start: 0.6516 (ptt90) cc_final: 0.6262 (ptt90) REVERT: B 587 MET cc_start: 0.7289 (mmm) cc_final: 0.6531 (mmm) REVERT: B 622 GLU cc_start: 0.7184 (tt0) cc_final: 0.6712 (tt0) REVERT: C 112 ASN cc_start: 0.7366 (t0) cc_final: 0.6855 (t0) REVERT: C 195 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: C 208 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7934 (mtp85) REVERT: C 562 ARG cc_start: 0.7995 (ptt-90) cc_final: 0.7409 (ttp80) REVERT: C 709 ASN cc_start: 0.8709 (m-40) cc_final: 0.8487 (m110) REVERT: H 96 LYS cc_start: 0.8556 (mptt) cc_final: 0.8321 (mtmm) REVERT: F 43 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: F 78 LYS cc_start: 0.8929 (mttt) cc_final: 0.8571 (mttt) REVERT: L 98 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7527 (mttm) REVERT: L 101 ARG cc_start: 0.7819 (ttt90) cc_final: 0.7331 (tpt170) REVERT: G 21 ILE cc_start: 0.8443 (mm) cc_final: 0.8120 (mt) REVERT: G 46 GLN cc_start: 0.8178 (mt0) cc_final: 0.7765 (mp10) outliers start: 65 outliers final: 52 residues processed: 348 average time/residue: 0.3451 time to fit residues: 182.3202 Evaluate side-chains 359 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 303 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 392 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 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 31 VAL 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 35 GLN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain 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 89 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 236 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** 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 = 0.3829 r_free = 0.3829 target = 0.145410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116168 restraints weight = 28387.713| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.33 r_work: 0.3210 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20052 Z= 0.251 Angle : 0.573 11.280 27267 Z= 0.304 Chirality : 0.043 0.160 2967 Planarity : 0.004 0.045 3519 Dihedral : 4.598 25.897 2733 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.63 % Allowed : 16.03 % Favored : 81.34 % 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: -0.45 (0.17), residues: 2418 helix: -0.69 (0.26), residues: 345 sheet: -0.22 (0.18), residues: 840 loop : -0.07 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 68 HIS 0.008 0.001 HIS B 534 PHE 0.024 0.002 PHE A 641 TYR 0.028 0.001 TYR B 689 ARG 0.007 0.000 ARG E 43 *********************** 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 369 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7344 (tp30) REVERT: A 233 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8209 (mm-30) REVERT: A 520 MET cc_start: 0.7770 (mmp) cc_final: 0.6592 (mmt) REVERT: A 536 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 562 ARG cc_start: 0.7810 (ttt90) cc_final: 0.6947 (ttp80) REVERT: A 638 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7177 (mtp-110) REVERT: A 677 MET cc_start: 0.8438 (mmt) cc_final: 0.8171 (mmp) REVERT: D 80 TYR cc_start: 0.8886 (m-80) cc_final: 0.8540 (m-80) REVERT: B 140 GLN cc_start: 0.6756 (tt0) cc_final: 0.6324 (tt0) REVERT: B 375 MET cc_start: 0.8473 (ttt) cc_final: 0.8210 (ttt) REVERT: B 562 ARG cc_start: 0.6482 (ptt90) cc_final: 0.6230 (ptt90) REVERT: B 587 MET cc_start: 0.7294 (mmm) cc_final: 0.6462 (mmm) REVERT: B 622 GLU cc_start: 0.7158 (tt0) cc_final: 0.6646 (tt0) REVERT: C 112 ASN cc_start: 0.7377 (t0) cc_final: 0.6879 (t0) REVERT: C 195 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: C 208 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.7851 (mtp85) REVERT: C 413 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8031 (mp) REVERT: C 562 ARG cc_start: 0.7946 (ptt-90) cc_final: 0.7393 (ttp80) REVERT: C 709 ASN cc_start: 0.8677 (m-40) cc_final: 0.8437 (m110) REVERT: C 714 LEU cc_start: 0.8285 (mt) cc_final: 0.8085 (mt) REVERT: H 96 LYS cc_start: 0.8533 (mptt) cc_final: 0.8305 (mtmm) REVERT: H 135 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8661 (p) REVERT: F 43 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: F 78 LYS cc_start: 0.8927 (mttt) cc_final: 0.8549 (mttt) REVERT: F 80 TYR cc_start: 0.8629 (m-80) cc_final: 0.8217 (m-10) REVERT: L 98 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7518 (mttm) REVERT: L 101 ARG cc_start: 0.7792 (ttt90) cc_final: 0.7319 (tpt170) REVERT: G 21 ILE cc_start: 0.8416 (mm) cc_final: 0.8066 (mt) REVERT: G 46 GLN cc_start: 0.8179 (mt0) cc_final: 0.7806 (mp10) REVERT: G 101 ARG cc_start: 0.7746 (mtm180) cc_final: 0.6683 (mmm-85) outliers start: 56 outliers final: 44 residues processed: 344 average time/residue: 0.3327 time to fit residues: 173.3217 Evaluate side-chains 349 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 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 567 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 413 ILE 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 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 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 175 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 25 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117017 restraints weight = 28158.934| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.32 r_work: 0.3223 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20052 Z= 0.219 Angle : 0.553 9.920 27267 Z= 0.293 Chirality : 0.042 0.156 2967 Planarity : 0.004 0.046 3519 Dihedral : 4.521 27.436 2733 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.97 % Allowed : 16.83 % 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: -0.27 (0.17), residues: 2418 helix: -0.35 (0.27), residues: 327 sheet: -0.14 (0.18), residues: 840 loop : 0.01 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 68 HIS 0.015 0.001 HIS C 516 PHE 0.022 0.002 PHE A 641 TYR 0.026 0.001 TYR B 689 ARG 0.008 0.000 ARG E 43 *********************** 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 350 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7233 (tp30) REVERT: A 233 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8161 (mm-30) REVERT: A 520 MET cc_start: 0.7728 (mmp) cc_final: 0.6584 (mmt) REVERT: A 562 ARG cc_start: 0.7832 (ttt90) cc_final: 0.6977 (ttp80) REVERT: A 638 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7367 (mtp-110) REVERT: A 677 MET cc_start: 0.8432 (mmt) cc_final: 0.8198 (mmp) REVERT: D 80 TYR cc_start: 0.8891 (m-80) cc_final: 0.8428 (m-80) REVERT: E 129 GLU cc_start: 0.5003 (tp30) cc_final: 0.4749 (mt-10) REVERT: B 140 GLN cc_start: 0.6778 (tt0) cc_final: 0.6314 (tt0) REVERT: B 375 MET cc_start: 0.8395 (ttt) cc_final: 0.8163 (ttt) REVERT: B 587 MET cc_start: 0.7264 (mmm) cc_final: 0.6501 (mmm) REVERT: C 112 ASN cc_start: 0.7323 (t0) cc_final: 0.6836 (t0) REVERT: C 195 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: C 208 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7747 (mtp85) REVERT: C 413 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 562 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.7328 (ttp80) REVERT: C 709 ASN cc_start: 0.8665 (m-40) cc_final: 0.8418 (m110) REVERT: H 96 LYS cc_start: 0.8517 (mptt) cc_final: 0.8294 (mtmm) REVERT: H 135 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8497 (p) REVERT: F 43 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: F 78 LYS cc_start: 0.8916 (mttt) cc_final: 0.8523 (mttt) REVERT: F 80 TYR cc_start: 0.8591 (m-80) cc_final: 0.8273 (m-10) REVERT: L 98 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7533 (mttm) REVERT: L 101 ARG cc_start: 0.7769 (ttt90) cc_final: 0.7308 (tpt170) REVERT: G 46 GLN cc_start: 0.8230 (mt0) cc_final: 0.7667 (mp10) outliers start: 42 outliers final: 32 residues processed: 331 average time/residue: 0.3310 time to fit residues: 164.4829 Evaluate side-chains 334 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 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 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 413 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 128 optimal weight: 0.0020 chunk 72 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 227 optimal weight: 0.0670 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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** B 129 GLN B 546 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118595 restraints weight = 28134.728| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.29 r_work: 0.3253 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20052 Z= 0.184 Angle : 0.544 9.445 27267 Z= 0.288 Chirality : 0.042 0.277 2967 Planarity : 0.004 0.046 3519 Dihedral : 4.386 25.623 2733 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.69 % Allowed : 17.49 % Favored : 80.82 % 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: -0.18 (0.17), residues: 2418 helix: -0.30 (0.27), residues: 327 sheet: -0.04 (0.18), residues: 840 loop : 0.03 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 539 HIS 0.010 0.001 HIS C 516 PHE 0.022 0.001 PHE C 650 TYR 0.026 0.001 TYR A 649 ARG 0.008 0.000 ARG E 43 ********************** 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 351 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7264 (tp30) REVERT: A 233 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 520 MET cc_start: 0.7717 (mmp) cc_final: 0.6577 (mmt) REVERT: A 562 ARG cc_start: 0.7794 (ttt90) cc_final: 0.6937 (ttp80) REVERT: A 638 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7337 (mtp-110) REVERT: A 677 MET cc_start: 0.8418 (mmt) cc_final: 0.8182 (mmp) REVERT: D 80 TYR cc_start: 0.8820 (m-80) cc_final: 0.8336 (m-80) REVERT: E 78 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7810 (ttp-110) REVERT: E 129 GLU cc_start: 0.4823 (tp30) cc_final: 0.4619 (mt-10) REVERT: B 140 GLN cc_start: 0.6714 (tt0) cc_final: 0.6291 (tt0) REVERT: B 562 ARG cc_start: 0.7150 (ptt90) cc_final: 0.6937 (ptt90) REVERT: B 587 MET cc_start: 0.7233 (mmm) cc_final: 0.6388 (mmm) REVERT: C 112 ASN cc_start: 0.7330 (t0) cc_final: 0.6852 (t0) REVERT: C 208 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7599 (mtp85) REVERT: C 413 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7967 (mp) REVERT: C 562 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7279 (ttp80) REVERT: C 709 ASN cc_start: 0.8631 (m-40) cc_final: 0.8366 (m110) REVERT: H 96 LYS cc_start: 0.8526 (mptt) cc_final: 0.8269 (mtmm) REVERT: H 135 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (p) REVERT: F 43 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: F 78 LYS cc_start: 0.8859 (mttt) cc_final: 0.8569 (mttt) REVERT: F 80 TYR cc_start: 0.8514 (m-80) cc_final: 0.8283 (m-10) REVERT: L 98 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7577 (mttm) REVERT: G 46 GLN cc_start: 0.8131 (mt0) cc_final: 0.7638 (mp10) REVERT: G 101 ARG cc_start: 0.7765 (mtm180) cc_final: 0.6677 (mmm-85) outliers start: 36 outliers final: 27 residues processed: 334 average time/residue: 0.3470 time to fit residues: 173.5615 Evaluate side-chains 333 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 2.482 ------------------------------------------------------------------------------- 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 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 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 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 413 ILE 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 94 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN E 69 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118719 restraints weight = 28295.202| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.32 r_work: 0.3248 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 20052 Z= 0.306 Angle : 0.711 59.196 27267 Z= 0.420 Chirality : 0.044 0.578 2967 Planarity : 0.004 0.050 3519 Dihedral : 4.369 25.703 2733 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.79 % Allowed : 17.49 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.17), residues: 2418 helix: -0.30 (0.27), residues: 327 sheet: -0.03 (0.18), residues: 840 loop : 0.02 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 68 HIS 0.009 0.001 HIS C 516 PHE 0.021 0.002 PHE C 650 TYR 0.023 0.001 TYR A 649 ARG 0.016 0.000 ARG F 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12878.77 seconds wall clock time: 228 minutes 27.54 seconds (13707.54 seconds total)