Starting phenix.real_space_refine on Mon May 19 22:02:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh0_19164/05_2025/8rh0_19164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh0_19164/05_2025/8rh0_19164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rh0_19164/05_2025/8rh0_19164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh0_19164/05_2025/8rh0_19164.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh0_19164/05_2025/8rh0_19164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh0_19164/05_2025/8rh0_19164.cif" } resolution = 3.44 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 12021 2.51 5 N 3387 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19137 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: "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: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 11.06, per 1000 atoms: 0.58 Number of scatterers: 19137 At special positions: 0 Unit cell: (185.231, 173.203, 174.406, 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 3636 8.00 N 3387 7.00 C 12021 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=2.06 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=2.07 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.05 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.07 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.05 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.06 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=2.07 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.10 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.05 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 101 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.6 seconds 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 47 sheets defined 18.1% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 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 306 through 310 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 removed outlier: 3.625A pdb=" N ARG A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 411 through 428 removed outlier: 4.302A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.586A pdb=" N ARG A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.558A pdb=" N ILE A 550 " --> pdb=" O ASN A 546 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'B' and resid 193 through 198 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 428 removed outlier: 4.625A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 543 removed outlier: 3.725A pdb=" N GLY B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.698A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 556 " --> pdb=" O SER B 552 " (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 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 716 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 306 through 310 removed outlier: 3.877A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 428 removed outlier: 4.320A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.711A pdb=" N LEU C 536 " --> pdb=" O GLN C 532 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.600A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 556 " --> pdb=" O SER C 552 " (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 removed outlier: 3.606A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 removed outlier: 3.516A pdb=" N ALA C 717 " --> pdb=" O ASP C 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.725A pdb=" N GLN H 70 " --> pdb=" O ARG H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 92 through 96 removed outlier: 3.777A pdb=" N THR H 96 " --> pdb=" O PHE H 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.536A pdb=" N SER L 29 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.841A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 30 removed outlier: 3.579A pdb=" N SER E 29 " --> pdb=" O ASN E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.867A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.951A pdb=" N GLU G 82 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 70 removed outlier: 3.662A pdb=" N GLN D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 67 through 70' Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.749A pdb=" N THR D 96 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 70 removed outlier: 3.682A pdb=" N GLN F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 70' Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.769A pdb=" N THR F 96 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.018A 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: 3.506A pdb=" N MET A 568 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.221A 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: 5.400A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 5.400A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 191 removed outlier: 5.532A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 184 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.016A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 324 " --> pdb=" O THR A 340 " (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: 5.414A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 4.923A 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: 4.205A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 568 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.757A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.601A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.601A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 191 removed outlier: 5.610A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 184 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.106A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 214 Processing sheet with id=AC2, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC3, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.927A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 666 through 667 removed outlier: 3.616A pdb=" N MET C 568 " --> pdb=" O VAL C 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.797A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.473A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.473A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 180 through 191 removed outlier: 5.594A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 184 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.304A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD3, first strand: chain 'C' and resid 210 through 214 Processing sheet with id=AD4, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.675A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 11 Processing sheet with id=AD8, first strand: chain 'H' and resid 15 through 16 removed outlier: 6.605A pdb=" N ILE H 39 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.735A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.735A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE3, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.685A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AE5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AE6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.810A pdb=" N VAL G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE8, first strand: chain 'D' and resid 8 through 11 Processing sheet with id=AE9, first strand: chain 'D' and resid 15 through 16 removed outlier: 5.798A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 8 through 11 Processing sheet with id=AF2, first strand: chain 'F' and resid 15 through 16 removed outlier: 6.653A pdb=" N ILE F 39 " --> pdb=" O TRP F 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP F 55 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP F 41 " --> pdb=" O MET F 53 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2190 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: 7.91 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6333 1.34 - 1.47: 5044 1.47 - 1.59: 8081 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 19602 Sorted by residual: bond pdb=" CE1 HIS A 308 " pdb=" NE2 HIS A 308 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS A 512 " pdb=" NE2 HIS A 512 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" CE1 HIS F 32 " pdb=" NE2 HIS F 32 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" NE ARG C 132 " pdb=" CZ ARG C 132 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.69e+01 bond pdb=" CE1 HIS B 692 " pdb=" NE2 HIS B 692 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 ... (remaining 19597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 26282 2.07 - 4.14: 335 4.14 - 6.20: 15 6.20 - 8.27: 4 8.27 - 10.34: 1 Bond angle restraints: 26637 Sorted by residual: angle pdb=" CA THR B 690 " pdb=" C THR B 690 " pdb=" O THR B 690 " ideal model delta sigma weight residual 121.99 118.12 3.87 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA ARG B 242 " pdb=" C ARG B 242 " pdb=" O ARG B 242 " ideal model delta sigma weight residual 121.84 118.13 3.71 1.16e+00 7.43e-01 1.02e+01 angle pdb=" CA THR B 241 " pdb=" C THR B 241 " pdb=" O THR B 241 " ideal model delta sigma weight residual 121.56 118.09 3.47 1.09e+00 8.42e-01 1.01e+01 angle pdb=" CA LEU A 601 " pdb=" C LEU A 601 " pdb=" O LEU A 601 " ideal model delta sigma weight residual 121.47 117.94 3.53 1.15e+00 7.56e-01 9.41e+00 angle pdb=" CA LEU A 564 " pdb=" CB LEU A 564 " pdb=" CG LEU A 564 " ideal model delta sigma weight residual 116.30 126.64 -10.34 3.50e+00 8.16e-02 8.73e+00 ... (remaining 26632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 10572 17.68 - 35.36: 813 35.36 - 53.03: 156 53.03 - 70.71: 61 70.71 - 88.39: 20 Dihedral angle restraints: 11622 sinusoidal: 4614 harmonic: 7008 Sorted by residual: dihedral pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " pdb=" SG CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sinusoidal sigma weight residual 93.00 10.67 82.33 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CA TYR E 49 " pdb=" C TYR E 49 " pdb=" N ASP E 50 " pdb=" CA ASP E 50 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA CYS A 573 " pdb=" C CYS A 573 " pdb=" N VAL A 574 " pdb=" CA VAL A 574 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1398 0.030 - 0.061: 954 0.061 - 0.091: 305 0.091 - 0.121: 186 0.121 - 0.152: 43 Chirality restraints: 2886 Sorted by residual: chirality pdb=" CA LEU A 601 " pdb=" N LEU A 601 " pdb=" C LEU A 601 " pdb=" CB LEU A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 675 " pdb=" N ILE A 675 " pdb=" C ILE A 675 " pdb=" CB ILE A 675 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL B 570 " pdb=" N VAL B 570 " pdb=" C VAL B 570 " pdb=" CB VAL B 570 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2883 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 512 " 0.032 2.00e-02 2.50e+03 2.98e-02 1.33e+01 pdb=" CG HIS A 512 " -0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS A 512 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 512 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 512 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 512 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 264 " 0.231 9.50e-02 1.11e+02 1.03e-01 6.73e+00 pdb=" NE ARG C 264 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 264 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 264 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 264 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 512 " 0.027 2.00e-02 2.50e+03 2.01e-02 6.09e+00 pdb=" CG HIS B 512 " -0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS B 512 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 HIS B 512 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS B 512 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS B 512 " 0.013 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1271 2.74 - 3.28: 17817 3.28 - 3.82: 30668 3.82 - 4.36: 37314 4.36 - 4.90: 66349 Nonbonded interactions: 153419 Sorted by model distance: nonbonded pdb=" OE2 GLU A 687 " pdb=" OG1 THR B 498 " model vdw 2.202 3.040 nonbonded pdb=" OG SER H 60 " pdb=" OD1 ASN H 62 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 380 " pdb=" OD2 ASP C 680 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR A 642 " pdb=" OD2 ASP B 566 " model vdw 2.229 3.040 nonbonded pdb=" O ASN C 202 " pdb=" NH2 ARG C 335 " model vdw 2.244 3.120 ... (remaining 153414 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.520 Find NCS groups from input model: 0.660 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.005 0.071 19623 Z= 0.311 Angle : 0.621 10.341 26679 Z= 0.361 Chirality : 0.048 0.152 2886 Planarity : 0.008 0.103 3483 Dihedral : 14.040 88.388 7083 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.19 (0.16), residues: 2397 helix: 0.59 (0.29), residues: 309 sheet: 0.73 (0.18), residues: 840 loop : -0.37 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP A 539 HIS 0.027 0.003 HIS A 512 PHE 0.025 0.003 PHE A 294 TYR 0.031 0.004 TYR B 303 ARG 0.026 0.002 ARG C 691 Details of bonding type rmsd hydrogen bonds : bond 0.11537 ( 735) hydrogen bonds : angle 5.86913 ( 2190) SS BOND : bond 0.02813 ( 21) SS BOND : angle 2.08586 ( 42) covalent geometry : bond 0.00491 (19602) covalent geometry : angle 0.61599 (26637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 2.232 Fit side-chains REVERT: B 568 MET cc_start: 0.7809 (ptp) cc_final: 0.7434 (ptp) REVERT: B 677 MET cc_start: 0.8459 (mmp) cc_final: 0.8123 (mmm) REVERT: C 653 TYR cc_start: 0.6305 (m-80) cc_final: 0.5791 (m-80) REVERT: C 677 MET cc_start: 0.8451 (mmm) cc_final: 0.7948 (mmm) REVERT: E 68 ASN cc_start: 0.8422 (m-40) cc_final: 0.8210 (m-40) REVERT: D 8 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7618 (mt0) REVERT: D 75 MET cc_start: 0.8804 (mtt) cc_final: 0.8529 (mtt) REVERT: D 92 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7740 (mtt-85) REVERT: D 115 ASP cc_start: 0.8423 (p0) cc_final: 0.7945 (t70) REVERT: F 75 MET cc_start: 0.9247 (mtt) cc_final: 0.8977 (mtt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3463 time to fit residues: 150.8865 Evaluate side-chains 224 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 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 129 GLN A 507 GLN A 511 ASN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101930 restraints weight = 29068.638| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.70 r_work: 0.3122 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19623 Z= 0.160 Angle : 0.545 13.266 26679 Z= 0.290 Chirality : 0.043 0.155 2886 Planarity : 0.004 0.036 3483 Dihedral : 4.232 22.170 2712 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.98 % Allowed : 6.88 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.34 (0.17), residues: 2397 helix: 0.84 (0.29), residues: 315 sheet: 0.77 (0.18), residues: 849 loop : -0.26 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.008 0.001 HIS A 534 PHE 0.016 0.001 PHE F 34 TYR 0.026 0.002 TYR L 48 ARG 0.005 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 735) hydrogen bonds : angle 4.96042 ( 2190) SS BOND : bond 0.00314 ( 21) SS BOND : angle 1.24666 ( 42) covalent geometry : bond 0.00377 (19602) covalent geometry : angle 0.54299 (26637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 1.941 Fit side-chains REVERT: A 456 LEU cc_start: 0.8237 (tp) cc_final: 0.8014 (tt) REVERT: A 568 MET cc_start: 0.7131 (mtm) cc_final: 0.6907 (ttm) REVERT: A 650 PHE cc_start: 0.6899 (m-80) cc_final: 0.6554 (m-10) REVERT: B 568 MET cc_start: 0.7800 (ptp) cc_final: 0.7031 (ptp) REVERT: B 641 PHE cc_start: 0.7780 (m-80) cc_final: 0.7556 (m-80) REVERT: B 677 MET cc_start: 0.8722 (mmp) cc_final: 0.8454 (mmm) REVERT: C 126 GLN cc_start: 0.6697 (tt0) cc_final: 0.6408 (tp40) REVERT: C 568 MET cc_start: 0.7020 (mtp) cc_final: 0.6634 (ttm) REVERT: C 653 TYR cc_start: 0.6720 (m-80) cc_final: 0.6278 (m-80) REVERT: C 677 MET cc_start: 0.8693 (mmm) cc_final: 0.8204 (mmm) REVERT: L 50 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (m-30) REVERT: E 68 ASN cc_start: 0.8635 (m-40) cc_final: 0.8285 (m-40) REVERT: D 8 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7613 (mt0) REVERT: D 92 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7544 (mtt-85) outliers start: 20 outliers final: 12 residues processed: 247 average time/residue: 0.3416 time to fit residues: 123.1799 Evaluate side-chains 225 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain D residue 56 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 54 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN A 534 HIS B 238 ASN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN C 580 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095908 restraints weight = 29717.359| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.67 r_work: 0.3039 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 19623 Z= 0.392 Angle : 0.714 12.162 26679 Z= 0.386 Chirality : 0.051 0.225 2886 Planarity : 0.006 0.058 3483 Dihedral : 4.938 23.721 2712 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.59 % Allowed : 9.76 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.30 (0.16), residues: 2397 helix: 0.04 (0.28), residues: 315 sheet: 0.32 (0.16), residues: 912 loop : -0.60 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 369 HIS 0.010 0.002 HIS H 32 PHE 0.023 0.003 PHE A 159 TYR 0.042 0.003 TYR L 48 ARG 0.007 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.05290 ( 735) hydrogen bonds : angle 5.28088 ( 2190) SS BOND : bond 0.00659 ( 21) SS BOND : angle 2.17362 ( 42) covalent geometry : bond 0.00943 (19602) covalent geometry : angle 0.70923 (26637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 2.157 Fit side-chains REVERT: A 112 ASN cc_start: 0.7525 (t0) cc_final: 0.7255 (t0) REVERT: A 601 LEU cc_start: 0.7732 (mt) cc_final: 0.7512 (mt) REVERT: A 650 PHE cc_start: 0.6975 (m-80) cc_final: 0.6548 (m-10) REVERT: B 178 ARG cc_start: 0.7822 (ptt90) cc_final: 0.7590 (mtp-110) REVERT: B 568 MET cc_start: 0.8040 (ptp) cc_final: 0.7430 (ptp) REVERT: B 641 PHE cc_start: 0.7886 (m-80) cc_final: 0.7668 (m-80) REVERT: B 663 ASP cc_start: 0.7287 (m-30) cc_final: 0.7053 (m-30) REVERT: C 412 CYS cc_start: 0.5228 (OUTLIER) cc_final: 0.4826 (t) REVERT: C 568 MET cc_start: 0.7244 (mtp) cc_final: 0.6563 (ttm) REVERT: C 677 MET cc_start: 0.8748 (mmm) cc_final: 0.8427 (mmm) REVERT: H 67 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7441 (mtm110) REVERT: L 59 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8139 (tm-30) REVERT: E 68 ASN cc_start: 0.8851 (m-40) cc_final: 0.8479 (m-40) REVERT: D 8 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7756 (mt0) outliers start: 53 outliers final: 40 residues processed: 247 average time/residue: 0.3400 time to fit residues: 124.1654 Evaluate side-chains 239 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 412 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 171 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** F 40 ASN ** 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 = 0.3587 r_free = 0.3587 target = 0.125392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100984 restraints weight = 29276.995| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.71 r_work: 0.3065 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19623 Z= 0.134 Angle : 0.515 13.941 26679 Z= 0.277 Chirality : 0.043 0.142 2886 Planarity : 0.004 0.044 3483 Dihedral : 4.385 24.773 2712 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.81 % Allowed : 11.81 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.06 (0.16), residues: 2397 helix: 0.67 (0.29), residues: 315 sheet: 0.58 (0.17), residues: 864 loop : -0.47 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.016 0.001 PHE F 34 TYR 0.021 0.001 TYR E 48 ARG 0.006 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 735) hydrogen bonds : angle 4.85162 ( 2190) SS BOND : bond 0.00430 ( 21) SS BOND : angle 1.32395 ( 42) covalent geometry : bond 0.00315 (19602) covalent geometry : angle 0.51243 (26637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7610 (t0) cc_final: 0.7326 (t0) REVERT: A 188 ASP cc_start: 0.8138 (t0) cc_final: 0.7881 (t0) REVERT: B 568 MET cc_start: 0.8055 (ptp) cc_final: 0.7513 (ptp) REVERT: C 568 MET cc_start: 0.7020 (mtp) cc_final: 0.6652 (ttm) REVERT: C 653 TYR cc_start: 0.6696 (m-80) cc_final: 0.6287 (m-80) REVERT: C 677 MET cc_start: 0.8791 (mmm) cc_final: 0.8279 (mmm) REVERT: H 67 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7433 (mtm110) REVERT: E 68 ASN cc_start: 0.8796 (m-40) cc_final: 0.8438 (m-40) REVERT: D 8 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7786 (mt0) REVERT: D 92 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7653 (mtt-85) outliers start: 37 outliers final: 26 residues processed: 261 average time/residue: 0.3372 time to fit residues: 130.5983 Evaluate side-chains 238 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 32 HIS ** F 40 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.123532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097627 restraints weight = 29547.248| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.87 r_work: 0.3052 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19623 Z= 0.199 Angle : 0.550 13.034 26679 Z= 0.295 Chirality : 0.044 0.165 2886 Planarity : 0.004 0.045 3483 Dihedral : 4.440 24.484 2712 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.68 % Allowed : 12.35 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.03 (0.16), residues: 2397 helix: 0.58 (0.29), residues: 315 sheet: 0.46 (0.17), residues: 882 loop : -0.48 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.019 0.002 PHE F 34 TYR 0.027 0.002 TYR E 48 ARG 0.009 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 735) hydrogen bonds : angle 4.86235 ( 2190) SS BOND : bond 0.00384 ( 21) SS BOND : angle 1.68073 ( 42) covalent geometry : bond 0.00476 (19602) covalent geometry : angle 0.54588 (26637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 2.300 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7552 (t0) cc_final: 0.7312 (t0) REVERT: A 188 ASP cc_start: 0.8108 (t0) cc_final: 0.7869 (t0) REVERT: A 534 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8287 (t-90) REVERT: B 568 MET cc_start: 0.8048 (ptp) cc_final: 0.7513 (ptp) REVERT: C 568 MET cc_start: 0.7096 (mtp) cc_final: 0.6673 (ttm) REVERT: C 653 TYR cc_start: 0.6816 (m-80) cc_final: 0.6403 (m-80) REVERT: C 677 MET cc_start: 0.8792 (mmm) cc_final: 0.8294 (mmm) REVERT: H 34 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8417 (t80) REVERT: H 67 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7397 (mtm110) REVERT: E 68 ASN cc_start: 0.8818 (m-40) cc_final: 0.8446 (m-40) REVERT: D 8 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7776 (mt0) REVERT: D 92 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7670 (mtt-85) outliers start: 55 outliers final: 46 residues processed: 258 average time/residue: 0.3463 time to fit residues: 133.0469 Evaluate side-chains 253 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 144 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099284 restraints weight = 29350.924| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.72 r_work: 0.3082 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19623 Z= 0.155 Angle : 0.512 14.388 26679 Z= 0.275 Chirality : 0.043 0.145 2886 Planarity : 0.004 0.044 3483 Dihedral : 4.323 23.786 2712 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.17 % Allowed : 12.54 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.06 (0.17), residues: 2397 helix: 0.71 (0.29), residues: 315 sheet: 0.51 (0.17), residues: 879 loop : -0.44 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.017 0.001 PHE F 34 TYR 0.021 0.001 TYR L 48 ARG 0.008 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 735) hydrogen bonds : angle 4.77353 ( 2190) SS BOND : bond 0.00386 ( 21) SS BOND : angle 1.36790 ( 42) covalent geometry : bond 0.00370 (19602) covalent geometry : angle 0.50956 (26637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7492 (t0) cc_final: 0.7284 (t0) REVERT: A 136 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.6818 (mtt90) REVERT: A 188 ASP cc_start: 0.8071 (t0) cc_final: 0.7844 (t0) REVERT: A 534 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: A 622 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: A 673 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 230 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 568 MET cc_start: 0.8001 (ptp) cc_final: 0.7487 (ptp) REVERT: B 641 PHE cc_start: 0.7839 (m-80) cc_final: 0.7637 (m-80) REVERT: B 651 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4309 (pm20) REVERT: C 568 MET cc_start: 0.7128 (mtp) cc_final: 0.6720 (ttm) REVERT: C 653 TYR cc_start: 0.6790 (m-80) cc_final: 0.6390 (m-80) REVERT: C 677 MET cc_start: 0.8790 (mmm) cc_final: 0.8303 (mmm) REVERT: H 34 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8385 (t80) REVERT: H 67 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7431 (mtm110) REVERT: G 48 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8195 (p90) REVERT: D 8 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7713 (mt0) REVERT: D 92 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7605 (mtt-85) outliers start: 65 outliers final: 48 residues processed: 275 average time/residue: 0.3352 time to fit residues: 137.5955 Evaluate side-chains 270 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 52 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.125083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100852 restraints weight = 29174.849| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.74 r_work: 0.3089 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19623 Z= 0.139 Angle : 0.501 14.481 26679 Z= 0.269 Chirality : 0.043 0.140 2886 Planarity : 0.004 0.041 3483 Dihedral : 4.222 22.453 2712 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.93 % Allowed : 13.27 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2397 helix: 0.81 (0.29), residues: 315 sheet: 0.63 (0.17), residues: 864 loop : -0.41 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.017 0.001 PHE F 34 TYR 0.020 0.001 TYR E 48 ARG 0.011 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 735) hydrogen bonds : angle 4.69752 ( 2190) SS BOND : bond 0.00437 ( 21) SS BOND : angle 1.49582 ( 42) covalent geometry : bond 0.00330 (19602) covalent geometry : angle 0.49832 (26637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7482 (t0) cc_final: 0.7266 (t0) REVERT: A 534 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.8156 (t-90) REVERT: A 622 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: A 673 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8523 (tt) REVERT: B 562 ARG cc_start: 0.7780 (ptm160) cc_final: 0.7470 (ptm-80) REVERT: B 568 MET cc_start: 0.8029 (ptp) cc_final: 0.7550 (ptp) REVERT: C 653 TYR cc_start: 0.6770 (m-80) cc_final: 0.6387 (m-80) REVERT: C 677 MET cc_start: 0.8716 (mmm) cc_final: 0.8315 (mmm) REVERT: H 34 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8377 (t80) REVERT: H 67 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7408 (mtm110) REVERT: D 8 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7748 (mt0) REVERT: D 24 ARG cc_start: 0.8582 (mtm110) cc_final: 0.8214 (ttm-80) REVERT: D 92 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7623 (mtt-85) outliers start: 60 outliers final: 50 residues processed: 277 average time/residue: 0.3266 time to fit residues: 134.9447 Evaluate side-chains 271 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100761 restraints weight = 29321.598| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.76 r_work: 0.3106 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19623 Z= 0.125 Angle : 0.495 14.943 26679 Z= 0.265 Chirality : 0.042 0.141 2886 Planarity : 0.004 0.041 3483 Dihedral : 4.170 22.420 2712 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.88 % Allowed : 13.76 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2397 helix: 0.91 (0.29), residues: 315 sheet: 0.67 (0.17), residues: 864 loop : -0.36 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.017 0.001 PHE A 194 TYR 0.019 0.001 TYR L 48 ARG 0.010 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 735) hydrogen bonds : angle 4.66125 ( 2190) SS BOND : bond 0.00403 ( 21) SS BOND : angle 1.43208 ( 42) covalent geometry : bond 0.00295 (19602) covalent geometry : angle 0.49243 (26637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 2.085 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7418 (t0) cc_final: 0.7177 (t0) REVERT: A 136 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6804 (mtt90) REVERT: A 375 MET cc_start: 0.8231 (tpp) cc_final: 0.7982 (mtp) REVERT: A 534 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.8087 (t-90) REVERT: A 622 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: A 673 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8462 (tt) REVERT: B 230 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (p) REVERT: B 562 ARG cc_start: 0.7702 (ptm160) cc_final: 0.7373 (ptm-80) REVERT: B 568 MET cc_start: 0.7964 (ptp) cc_final: 0.7453 (ptp) REVERT: C 653 TYR cc_start: 0.6726 (m-80) cc_final: 0.6326 (m-80) REVERT: C 677 MET cc_start: 0.8787 (mmm) cc_final: 0.8388 (mmm) REVERT: H 67 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7415 (mtm110) REVERT: D 8 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7684 (mt0) REVERT: D 24 ARG cc_start: 0.8551 (mtm110) cc_final: 0.8169 (ttm-80) REVERT: D 89 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: D 92 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7478 (mtt-85) outliers start: 59 outliers final: 48 residues processed: 273 average time/residue: 0.3488 time to fit residues: 141.5160 Evaluate side-chains 271 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098175 restraints weight = 29489.552| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.86 r_work: 0.3045 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19623 Z= 0.221 Angle : 0.566 15.316 26679 Z= 0.303 Chirality : 0.045 0.167 2886 Planarity : 0.005 0.054 3483 Dihedral : 4.450 22.727 2712 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.17 % Allowed : 13.81 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.05 (0.17), residues: 2397 helix: 0.64 (0.29), residues: 315 sheet: 0.53 (0.17), residues: 873 loop : -0.45 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 52 HIS 0.005 0.001 HIS B 534 PHE 0.020 0.002 PHE F 34 TYR 0.028 0.002 TYR L 48 ARG 0.011 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 735) hydrogen bonds : angle 4.88176 ( 2190) SS BOND : bond 0.00425 ( 21) SS BOND : angle 1.60045 ( 42) covalent geometry : bond 0.00532 (19602) covalent geometry : angle 0.56293 (26637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 2.074 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7503 (t0) cc_final: 0.7289 (t0) REVERT: A 534 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (t-90) REVERT: A 616 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7620 (tp-100) REVERT: A 622 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: A 673 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 230 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8433 (p) REVERT: B 568 MET cc_start: 0.8042 (ptp) cc_final: 0.7609 (ptp) REVERT: C 297 MET cc_start: 0.8985 (ttp) cc_final: 0.8638 (ptt) REVERT: C 653 TYR cc_start: 0.6838 (m-80) cc_final: 0.6393 (m-80) REVERT: C 677 MET cc_start: 0.8725 (mmm) cc_final: 0.8331 (mmm) REVERT: H 34 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8376 (t80) REVERT: D 8 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7796 (mt0) REVERT: D 92 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7615 (mtt-85) outliers start: 65 outliers final: 53 residues processed: 271 average time/residue: 0.3361 time to fit residues: 135.6960 Evaluate side-chains 269 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 230 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100983 restraints weight = 29248.934| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.71 r_work: 0.3105 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19623 Z= 0.125 Angle : 0.507 15.168 26679 Z= 0.271 Chirality : 0.043 0.167 2886 Planarity : 0.004 0.044 3483 Dihedral : 4.232 22.618 2712 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.54 % Allowed : 14.40 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.21 (0.17), residues: 2397 helix: 0.91 (0.30), residues: 312 sheet: 0.65 (0.17), residues: 864 loop : -0.39 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 PHE 0.016 0.001 PHE F 34 TYR 0.018 0.001 TYR L 48 ARG 0.011 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 735) hydrogen bonds : angle 4.69822 ( 2190) SS BOND : bond 0.00374 ( 21) SS BOND : angle 1.57450 ( 42) covalent geometry : bond 0.00293 (19602) covalent geometry : angle 0.50399 (26637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 2.703 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7410 (t0) cc_final: 0.7195 (t0) REVERT: A 183 MET cc_start: 0.8700 (mmt) cc_final: 0.8295 (mmt) REVERT: A 375 MET cc_start: 0.8204 (tpp) cc_final: 0.7850 (mtp) REVERT: A 534 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.8121 (t-90) REVERT: A 622 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: A 673 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8477 (tt) REVERT: B 230 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 562 ARG cc_start: 0.8011 (ptm-80) cc_final: 0.7520 (ptm160) REVERT: B 568 MET cc_start: 0.7939 (ptp) cc_final: 0.7281 (ptp) REVERT: C 297 MET cc_start: 0.8887 (ttp) cc_final: 0.8612 (ptt) REVERT: C 653 TYR cc_start: 0.6736 (m-80) cc_final: 0.6341 (m-80) REVERT: C 677 MET cc_start: 0.8731 (mmm) cc_final: 0.8354 (mmm) REVERT: D 8 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7673 (mt0) REVERT: D 24 ARG cc_start: 0.8495 (mtm110) cc_final: 0.8130 (ttm-80) REVERT: D 89 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: D 92 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7559 (mtt-85) outliers start: 52 outliers final: 47 residues processed: 261 average time/residue: 0.3403 time to fit residues: 133.5978 Evaluate side-chains 264 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 48 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099155 restraints weight = 29552.168| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.76 r_work: 0.3070 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19623 Z= 0.201 Angle : 0.555 15.169 26679 Z= 0.297 Chirality : 0.045 0.163 2886 Planarity : 0.004 0.051 3483 Dihedral : 4.386 22.872 2712 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.93 % Allowed : 14.06 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.05 (0.17), residues: 2397 helix: 0.72 (0.29), residues: 315 sheet: 0.49 (0.17), residues: 882 loop : -0.43 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 52 HIS 0.005 0.001 HIS B 534 PHE 0.020 0.002 PHE F 34 TYR 0.026 0.002 TYR L 48 ARG 0.010 0.000 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 735) hydrogen bonds : angle 4.80910 ( 2190) SS BOND : bond 0.00393 ( 21) SS BOND : angle 1.89709 ( 42) covalent geometry : bond 0.00484 (19602) covalent geometry : angle 0.55063 (26637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10381.10 seconds wall clock time: 180 minutes 5.68 seconds (10805.68 seconds total)