Starting phenix.real_space_refine on Wed Jan 22 20:19:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh0_19164/01_2025/8rh0_19164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh0_19164/01_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_19164/01_2025/8rh0_19164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh0_19164/01_2025/8rh0_19164.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh0_19164/01_2025/8rh0_19164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh0_19164/01_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-5571/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: 10.28, per 1000 atoms: 0.54 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: 4.64 Conformation dependent library (CDL) restraints added in 2.3 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: 3.03 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: 8.11 Time building geometry restraints manager: 5.27 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: 0.04 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: 1.600 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.580 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.530 ------------------------------------------------------------------------------- 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 0.045 19602 Z= 0.323 Angle : 0.616 10.341 26637 Z= 0.359 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 *********************** 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 : 2.140 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: 0.3586 time to fit residues: 156.7331 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 : 2.129 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 3.9990 chunk 185 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 A 532 GLN B 238 ASN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 534 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102352 restraints weight = 29139.984| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.78 r_work: 0.3097 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19602 Z= 0.299 Angle : 0.564 13.330 26637 Z= 0.302 Chirality : 0.044 0.172 2886 Planarity : 0.004 0.038 3483 Dihedral : 4.304 22.242 2712 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.02 % Allowed : 7.32 % Favored : 91.65 % 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: 0.27 (0.16), residues: 2397 helix: 0.74 (0.29), residues: 315 sheet: 0.73 (0.18), residues: 849 loop : -0.31 (0.16), 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 0.017 0.002 PHE F 34 TYR 0.029 0.002 TYR G 48 ARG 0.005 0.001 ARG E 60 *********************** 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 261 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 2.098 Fit side-chains REVERT: A 366 MET cc_start: 0.8173 (mmt) cc_final: 0.7705 (mmt) REVERT: A 456 LEU cc_start: 0.8286 (tp) cc_final: 0.8068 (tt) REVERT: A 601 LEU cc_start: 0.7544 (mt) cc_final: 0.7290 (mt) REVERT: A 650 PHE cc_start: 0.7007 (m-80) cc_final: 0.6656 (m-10) REVERT: B 568 MET cc_start: 0.7906 (ptp) cc_final: 0.7191 (ptp) REVERT: B 641 PHE cc_start: 0.7871 (m-80) cc_final: 0.7667 (m-80) REVERT: B 663 ASP cc_start: 0.7254 (m-30) cc_final: 0.7005 (m-30) REVERT: C 126 GLN cc_start: 0.6777 (tt0) cc_final: 0.6503 (tp40) REVERT: C 568 MET cc_start: 0.7117 (mtp) cc_final: 0.6698 (ttm) REVERT: C 653 TYR cc_start: 0.6779 (m-80) cc_final: 0.6325 (m-80) REVERT: C 677 MET cc_start: 0.8709 (mmm) cc_final: 0.8219 (mmm) REVERT: E 68 ASN cc_start: 0.8677 (m-40) cc_final: 0.8342 (m-40) REVERT: D 8 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7767 (mt0) REVERT: D 92 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7587 (mtt-85) outliers start: 21 outliers final: 14 residues processed: 251 average time/residue: 0.3658 time to fit residues: 134.2772 Evaluate side-chains 227 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 2.078 ------------------------------------------------------------------------------- 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 501 ILE 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 71 THR 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: 0.9990 chunk 119 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 534 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.3537 r_free = 0.3537 target = 0.121745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096444 restraints weight = 29684.152| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.68 r_work: 0.3039 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 19602 Z= 0.570 Angle : 0.686 13.581 26637 Z= 0.371 Chirality : 0.050 0.227 2886 Planarity : 0.006 0.051 3483 Dihedral : 4.904 22.891 2712 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.54 % Allowed : 10.30 % Favored : 87.16 % 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: 0.03 (0.28), residues: 315 sheet: 0.30 (0.16), residues: 912 loop : -0.59 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 369 HIS 0.010 0.002 HIS H 32 PHE 0.022 0.002 PHE A 159 TYR 0.041 0.003 TYR L 48 ARG 0.006 0.001 ARG B 335 *********************** 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 262 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 2.013 Fit side-chains REVERT: A 112 ASN cc_start: 0.7562 (t0) cc_final: 0.7290 (t0) REVERT: A 601 LEU cc_start: 0.7975 (mt) cc_final: 0.7682 (mt) REVERT: A 650 PHE cc_start: 0.6964 (m-80) cc_final: 0.6544 (m-80) REVERT: B 178 ARG cc_start: 0.7816 (ptt90) cc_final: 0.7601 (mtp-110) REVERT: B 568 MET cc_start: 0.8060 (ptp) cc_final: 0.7465 (ptp) REVERT: B 641 PHE cc_start: 0.7885 (m-80) cc_final: 0.7675 (m-80) REVERT: C 412 CYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4874 (t) REVERT: C 568 MET cc_start: 0.7152 (mtp) cc_final: 0.6511 (ttm) REVERT: C 677 MET cc_start: 0.8751 (mmm) cc_final: 0.8443 (mmm) REVERT: H 67 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7448 (mtm110) REVERT: E 68 ASN cc_start: 0.8882 (m-40) cc_final: 0.8514 (m-40) REVERT: D 8 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7757 (mt0) REVERT: D 92 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7529 (mtt-85) outliers start: 52 outliers final: 39 residues processed: 246 average time/residue: 0.3686 time to fit residues: 134.6420 Evaluate side-chains 242 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 2.049 ------------------------------------------------------------------------------- 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 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 53 MET 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 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: 0.5980 chunk 170 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101589 restraints weight = 29275.961| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.74 r_work: 0.3069 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19602 Z= 0.192 Angle : 0.504 13.932 26637 Z= 0.272 Chirality : 0.043 0.140 2886 Planarity : 0.004 0.043 3483 Dihedral : 4.328 22.679 2712 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.81 % Allowed : 11.86 % Favored : 86.33 % 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: 0.08 (0.16), residues: 2397 helix: 0.68 (0.29), residues: 315 sheet: 0.58 (0.17), residues: 864 loop : -0.45 (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 A 624 *********************** 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 : 2.131 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7623 (t0) cc_final: 0.7335 (t0) REVERT: A 188 ASP cc_start: 0.8148 (t0) cc_final: 0.7892 (t0) REVERT: A 604 PHE cc_start: 0.7858 (p90) cc_final: 0.7308 (p90) REVERT: B 568 MET cc_start: 0.8076 (ptp) cc_final: 0.7543 (ptp) REVERT: C 568 MET cc_start: 0.6999 (mtp) cc_final: 0.6692 (ttm) REVERT: C 653 TYR cc_start: 0.6680 (m-80) cc_final: 0.6278 (m-80) REVERT: C 677 MET cc_start: 0.8811 (mmm) cc_final: 0.8319 (mmm) REVERT: H 67 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7453 (mtm110) REVERT: E 68 ASN cc_start: 0.8799 (m-40) cc_final: 0.8433 (m-40) REVERT: D 8 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7776 (mt0) REVERT: D 92 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7573 (mtt-85) outliers start: 37 outliers final: 28 residues processed: 264 average time/residue: 0.3523 time to fit residues: 137.5551 Evaluate side-chains 238 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 A residue 582 ILE 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 170 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 676 THR 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 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 55 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: 0.9990 chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098134 restraints weight = 29777.784| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.75 r_work: 0.3023 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19602 Z= 0.481 Angle : 0.616 14.307 26637 Z= 0.333 Chirality : 0.047 0.198 2886 Planarity : 0.005 0.051 3483 Dihedral : 4.686 23.126 2712 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.37 % Allowed : 11.96 % Favored : 84.68 % 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: -0.29 (0.16), residues: 2397 helix: 0.24 (0.29), residues: 315 sheet: 0.31 (0.17), residues: 882 loop : -0.63 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 52 HIS 0.007 0.002 HIS B 534 PHE 0.023 0.002 PHE F 34 TYR 0.034 0.002 TYR L 48 ARG 0.007 0.001 ARG C 599 *********************** 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 282 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 213 time to evaluate : 2.084 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7568 (t0) cc_final: 0.7334 (t0) REVERT: A 188 ASP cc_start: 0.8197 (t0) cc_final: 0.7953 (t0) REVERT: A 534 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8237 (t-90) REVERT: A 622 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: B 366 MET cc_start: 0.8596 (mmt) cc_final: 0.8280 (mmt) REVERT: B 568 MET cc_start: 0.8069 (ptp) cc_final: 0.7515 (ptp) REVERT: C 599 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7402 (mmm160) REVERT: C 653 TYR cc_start: 0.6909 (m-80) cc_final: 0.6466 (m-80) REVERT: C 677 MET cc_start: 0.8826 (mmm) cc_final: 0.8321 (mmm) REVERT: H 34 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8274 (t80) REVERT: H 67 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7407 (mtm110) REVERT: L 19 ARG cc_start: 0.8603 (ttm110) cc_final: 0.8376 (ttm110) REVERT: E 68 ASN cc_start: 0.8862 (m-40) cc_final: 0.8505 (m-40) REVERT: D 8 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7807 (mt0) REVERT: F 85 TYR cc_start: 0.8875 (m-80) cc_final: 0.8611 (m-80) outliers start: 69 outliers final: 52 residues processed: 265 average time/residue: 0.3811 time to fit residues: 150.5272 Evaluate side-chains 262 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 2.336 ------------------------------------------------------------------------------- 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 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 135 THR Chi-restraints excluded: chain B residue 170 VAL 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 492 VAL Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 125 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 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 5 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 12 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 44 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 144 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** 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 = 0.3576 r_free = 0.3576 target = 0.124715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099739 restraints weight = 29351.877| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.74 r_work: 0.3092 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19602 Z= 0.206 Angle : 0.496 13.538 26637 Z= 0.268 Chirality : 0.043 0.145 2886 Planarity : 0.004 0.046 3483 Dihedral : 4.304 22.926 2712 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.44 % Allowed : 13.76 % 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: 0.01 (0.17), residues: 2397 helix: 0.70 (0.29), residues: 315 sheet: 0.49 (0.17), residues: 876 loop : -0.48 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 PHE 0.017 0.001 PHE F 34 TYR 0.019 0.001 TYR L 48 ARG 0.005 0.000 ARG F 89 *********************** 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 272 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8212 (t-90) REVERT: A 673 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8553 (tt) REVERT: B 230 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 366 MET cc_start: 0.8502 (mmt) cc_final: 0.8166 (mmt) REVERT: B 568 MET cc_start: 0.7972 (ptp) cc_final: 0.7420 (ptp) REVERT: B 651 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5287 (pm20) REVERT: C 568 MET cc_start: 0.7038 (mtp) cc_final: 0.6697 (ttm) REVERT: C 653 TYR cc_start: 0.6696 (m-80) cc_final: 0.6304 (m-80) REVERT: C 677 MET cc_start: 0.8819 (mmm) cc_final: 0.8360 (mmm) REVERT: H 34 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8394 (t80) REVERT: H 67 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7421 (mtm110) REVERT: L 19 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8343 (ttm110) REVERT: D 8 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7703 (mt0) REVERT: F 85 TYR cc_start: 0.8722 (m-80) cc_final: 0.8450 (m-80) outliers start: 50 outliers final: 39 residues processed: 264 average time/residue: 0.3701 time to fit residues: 143.0470 Evaluate side-chains 254 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 582 ILE Chi-restraints excluded: chain A residue 583 VAL 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 347 THR Chi-restraints excluded: chain B residue 512 HIS 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 52 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 161 optimal weight: 0.2980 chunk 224 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** 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 11 GLN 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 = 0.125637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101292 restraints weight = 29169.850| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.72 r_work: 0.3102 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19602 Z= 0.185 Angle : 0.486 14.862 26637 Z= 0.261 Chirality : 0.042 0.141 2886 Planarity : 0.004 0.044 3483 Dihedral : 4.145 22.669 2712 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.59 % Allowed : 13.91 % Favored : 83.50 % 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: 0.89 (0.29), residues: 315 sheet: 0.71 (0.17), residues: 855 loop : -0.39 (0.17), residues: 1227 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 0.019 0.001 TYR L 48 ARG 0.007 0.000 ARG F 89 *********************** 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 284 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.8089 (t-90) REVERT: A 673 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8489 (tt) REVERT: B 230 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8417 (p) REVERT: B 366 MET cc_start: 0.8503 (mmt) cc_final: 0.8136 (mmt) REVERT: B 429 TYR cc_start: 0.7768 (m-10) cc_final: 0.7565 (m-10) REVERT: B 568 MET cc_start: 0.7905 (ptp) cc_final: 0.7285 (ptp) REVERT: B 651 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5360 (pm20) REVERT: C 419 ASP cc_start: 0.7662 (m-30) cc_final: 0.7457 (m-30) REVERT: C 568 MET cc_start: 0.7007 (mtp) cc_final: 0.6747 (ttm) REVERT: C 653 TYR cc_start: 0.6629 (m-80) cc_final: 0.6212 (m-80) REVERT: C 677 MET cc_start: 0.8748 (mmm) cc_final: 0.8370 (mmm) REVERT: H 34 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8334 (t80) REVERT: H 67 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7428 (mtm110) REVERT: G 48 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8179 (p90) REVERT: G 59 GLU cc_start: 0.7893 (tp30) cc_final: 0.7686 (tp30) REVERT: D 8 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7699 (mt0) REVERT: D 24 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8203 (ttm-80) REVERT: D 89 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8064 (mtm180) REVERT: D 92 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7540 (mtt-85) outliers start: 53 outliers final: 42 residues processed: 272 average time/residue: 0.3612 time to fit residues: 145.7114 Evaluate side-chains 267 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 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 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 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 347 THR 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 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 96 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 42 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 76 THR 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: 3.9990 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 218 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN H 40 ASN D 32 HIS ** D 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 = 0.3609 r_free = 0.3609 target = 0.127089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102867 restraints weight = 29219.967| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.69 r_work: 0.3122 rms_B_bonded: 1.94 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: 0.8321 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19602 Z= 0.156 Angle : 0.471 14.927 26637 Z= 0.252 Chirality : 0.042 0.147 2886 Planarity : 0.004 0.046 3483 Dihedral : 4.024 22.345 2712 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.64 % Allowed : 14.15 % Favored : 83.21 % 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: 0.39 (0.17), residues: 2397 helix: 1.07 (0.30), residues: 312 sheet: 0.78 (0.18), residues: 855 loop : -0.28 (0.17), residues: 1230 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 0.014 0.001 PHE F 34 TYR 0.016 0.001 TYR L 48 ARG 0.008 0.000 ARG C 599 *********************** 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 289 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8183 (tpp) cc_final: 0.7912 (mtp) REVERT: A 534 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (t-90) REVERT: A 622 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: A 624 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7022 (mtp85) REVERT: A 673 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 230 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 366 MET cc_start: 0.8460 (mmt) cc_final: 0.8060 (mmt) REVERT: B 562 ARG cc_start: 0.8020 (ptm-80) cc_final: 0.7503 (ptm160) REVERT: B 568 MET cc_start: 0.7887 (ptp) cc_final: 0.7274 (ptp) REVERT: B 651 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5420 (pm20) REVERT: C 131 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7935 (mtt-85) REVERT: C 653 TYR cc_start: 0.6574 (m-80) cc_final: 0.6175 (m-80) REVERT: C 677 MET cc_start: 0.8781 (mmm) cc_final: 0.8424 (mmm) REVERT: H 34 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8331 (t80) REVERT: H 67 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7402 (mtm110) REVERT: G 59 GLU cc_start: 0.7893 (tp30) cc_final: 0.7691 (tp30) REVERT: D 8 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7671 (mt0) REVERT: D 24 ARG cc_start: 0.8516 (mtm110) cc_final: 0.8226 (ttm-80) REVERT: D 89 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.8073 (mtm180) REVERT: D 92 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7500 (mtt-85) outliers start: 54 outliers final: 41 residues processed: 279 average time/residue: 0.3532 time to fit residues: 145.1027 Evaluate side-chains 272 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL 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 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 347 THR Chi-restraints excluded: chain B residue 512 HIS 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 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 534 HIS 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 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 10 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 16 VAL 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: 5.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 14 optimal weight: 0.0570 chunk 99 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- 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** B 657 HIS C 129 GLN D 32 HIS ** D 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 = 0.3574 r_free = 0.3574 target = 0.124520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099705 restraints weight = 29425.025| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.71 r_work: 0.3081 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19602 Z= 0.290 Angle : 0.531 15.228 26637 Z= 0.284 Chirality : 0.044 0.162 2886 Planarity : 0.004 0.049 3483 Dihedral : 4.247 22.500 2712 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 0.21 (0.17), residues: 2397 helix: 0.79 (0.29), residues: 315 sheet: 0.67 (0.17), residues: 864 loop : -0.37 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 52 HIS 0.005 0.001 HIS B 534 PHE 0.019 0.002 PHE F 34 TYR 0.025 0.002 TYR L 48 ARG 0.009 0.000 ARG F 89 *********************** 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: 60 poor density : 221 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8174 (t-90) REVERT: A 616 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7361 (tp-100) REVERT: A 622 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: A 624 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6999 (mtp85) REVERT: A 673 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 230 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8345 (p) REVERT: B 366 MET cc_start: 0.8458 (mmt) cc_final: 0.8051 (mmt) REVERT: B 562 ARG cc_start: 0.8075 (ptm-80) cc_final: 0.7855 (ptm-80) REVERT: B 568 MET cc_start: 0.7896 (ptp) cc_final: 0.7249 (ptp) REVERT: B 651 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: C 421 MET cc_start: 0.7040 (mtm) cc_final: 0.6531 (mtm) REVERT: C 653 TYR cc_start: 0.6751 (m-80) cc_final: 0.6336 (m-80) REVERT: C 677 MET cc_start: 0.8782 (mmm) cc_final: 0.8393 (mmm) REVERT: H 34 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8334 (t80) REVERT: G 48 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.7964 (p90) REVERT: D 8 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7690 (mt0) REVERT: D 24 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8071 (ttm-80) REVERT: D 92 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7523 (mtt-85) outliers start: 60 outliers final: 48 residues processed: 271 average time/residue: 0.3572 time to fit residues: 142.3347 Evaluate side-chains 273 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL 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 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 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 512 HIS 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 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 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 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 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: 2.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 210 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 HIS 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 = 0.3590 r_free = 0.3590 target = 0.125706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101502 restraints weight = 29309.471| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.78 r_work: 0.3097 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19602 Z= 0.189 Angle : 0.495 15.269 26637 Z= 0.264 Chirality : 0.042 0.157 2886 Planarity : 0.004 0.045 3483 Dihedral : 4.118 22.369 2712 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.59 % Allowed : 14.45 % Favored : 82.97 % 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: 0.34 (0.17), residues: 2397 helix: 0.95 (0.30), residues: 312 sheet: 0.76 (0.17), residues: 858 loop : -0.29 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.009 0.001 HIS B 534 PHE 0.016 0.001 PHE F 34 TYR 0.018 0.001 TYR L 48 ARG 0.008 0.000 ARG F 89 ********************** 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 280 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8240 (tpp) cc_final: 0.7901 (mtp) REVERT: A 534 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8160 (t-90) REVERT: A 622 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: A 624 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7026 (mtp85) REVERT: A 673 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (tt) REVERT: B 230 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 366 MET cc_start: 0.8507 (mmt) cc_final: 0.8121 (mmt) REVERT: B 562 ARG cc_start: 0.8041 (ptm-80) cc_final: 0.7558 (ptm160) REVERT: B 568 MET cc_start: 0.7984 (ptp) cc_final: 0.7387 (ptp) REVERT: B 651 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5577 (pm20) REVERT: C 653 TYR cc_start: 0.6601 (m-80) cc_final: 0.6192 (m-80) REVERT: C 677 MET cc_start: 0.8776 (mmm) cc_final: 0.8435 (mmm) REVERT: H 34 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8330 (t80) REVERT: D 8 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7766 (mt0) REVERT: D 24 ARG cc_start: 0.8442 (mtm110) cc_final: 0.8116 (ttm-80) REVERT: D 92 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7634 (mtt-85) outliers start: 53 outliers final: 46 residues processed: 270 average time/residue: 0.3590 time to fit residues: 143.5894 Evaluate side-chains 275 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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 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 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 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 512 HIS 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 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 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 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 10 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 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** 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 = 0.3590 r_free = 0.3590 target = 0.125631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101308 restraints weight = 29462.346| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.79 r_work: 0.3089 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19602 Z= 0.213 Angle : 0.501 15.330 26637 Z= 0.267 Chirality : 0.043 0.157 2886 Planarity : 0.004 0.045 3483 Dihedral : 4.126 22.335 2712 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 14.40 % 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: 0.31 (0.17), residues: 2397 helix: 0.95 (0.30), residues: 312 sheet: 0.71 (0.17), residues: 864 loop : -0.31 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.003 0.001 HIS B 516 PHE 0.017 0.001 PHE F 34 TYR 0.020 0.001 TYR L 48 ARG 0.007 0.000 ARG C 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10195.11 seconds wall clock time: 182 minutes 13.53 seconds (10933.53 seconds total)