Starting phenix.real_space_refine on Thu Sep 18 18:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh0_19164/09_2025/8rh0_19164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh0_19164/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rh0_19164/09_2025/8rh0_19164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh0_19164/09_2025/8rh0_19164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rh0_19164/09_2025/8rh0_19164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh0_19164/09_2025/8rh0_19164.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.28, per 1000 atoms: 0.22 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: 1.37 Conformation dependent library (CDL) restraints added in 709.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.81 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: 3.27 Time building geometry restraints manager: 1.81 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.080 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19623 Z= 0.311 Angle : 0.621 10.341 26679 Z= 0.361 Chirality : 0.048 0.152 2886 Planarity : 0.008 0.103 3483 Dihedral : 14.040 88.388 7083 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (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 ARG 0.026 0.002 ARG C 691 TYR 0.031 0.004 TYR B 303 PHE 0.025 0.003 PHE A 294 TRP 0.027 0.005 TRP A 539 HIS 0.027 0.003 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00491 (19602) covalent geometry : angle 0.61599 (26637) SS BOND : bond 0.02813 ( 21) SS BOND : angle 2.08586 ( 42) hydrogen bonds : bond 0.11537 ( 735) hydrogen bonds : angle 5.86913 ( 2190) *********************** 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 : 0.645 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: 0.1603 time to fit residues: 70.0549 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 : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101512 restraints weight = 29133.070| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.71 r_work: 0.3115 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.004 0.050 19623 Z= 0.169 Angle : 0.553 13.253 26679 Z= 0.295 Chirality : 0.044 0.165 2886 Planarity : 0.004 0.037 3483 Dihedral : 4.268 22.214 2712 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.02 % Allowed : 7.08 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2397 helix: 0.79 (0.29), residues: 315 sheet: 0.75 (0.18), residues: 849 loop : -0.28 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 89 TYR 0.027 0.002 TYR G 48 PHE 0.016 0.001 PHE F 34 TRP 0.014 0.002 TRP H 52 HIS 0.008 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00399 (19602) covalent geometry : angle 0.55065 (26637) SS BOND : bond 0.00327 ( 21) SS BOND : angle 1.27304 ( 42) hydrogen bonds : bond 0.04215 ( 735) hydrogen bonds : angle 4.95464 ( 2190) *********************** 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 260 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.676 Fit side-chains REVERT: A 366 MET cc_start: 0.8089 (mmt) cc_final: 0.7598 (mmt) REVERT: A 568 MET cc_start: 0.7107 (mtm) cc_final: 0.6877 (ttm) REVERT: A 601 LEU cc_start: 0.7430 (mt) cc_final: 0.7158 (mt) REVERT: A 650 PHE cc_start: 0.6856 (m-80) cc_final: 0.6542 (m-10) REVERT: B 568 MET cc_start: 0.7754 (ptp) cc_final: 0.6983 (ptp) REVERT: B 641 PHE cc_start: 0.7755 (m-80) cc_final: 0.7525 (m-80) REVERT: B 663 ASP cc_start: 0.7194 (m-30) cc_final: 0.6920 (m-30) REVERT: C 126 GLN cc_start: 0.6716 (tt0) cc_final: 0.6411 (tp40) REVERT: C 568 MET cc_start: 0.6970 (mtp) cc_final: 0.6624 (ttm) REVERT: C 653 TYR cc_start: 0.6732 (m-80) cc_final: 0.6282 (m-80) REVERT: C 677 MET cc_start: 0.8692 (mmm) cc_final: 0.8190 (mmm) REVERT: E 68 ASN cc_start: 0.8644 (m-40) cc_final: 0.8287 (m-40) REVERT: D 8 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7688 (mt0) REVERT: D 92 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7508 (mtt-85) outliers start: 21 outliers final: 13 residues processed: 250 average time/residue: 0.1576 time to fit residues: 57.5476 Evaluate side-chains 225 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 99 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 205 optimal weight: 0.0070 chunk 224 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 238 ASN ** 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 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 = 0.3573 r_free = 0.3573 target = 0.124430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099957 restraints weight = 29595.931| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.80 r_work: 0.3049 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19623 Z= 0.238 Angle : 0.588 13.484 26679 Z= 0.317 Chirality : 0.046 0.185 2886 Planarity : 0.005 0.055 3483 Dihedral : 4.504 22.493 2712 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.10 % Allowed : 9.03 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 2397 helix: 0.51 (0.29), residues: 315 sheet: 0.60 (0.17), residues: 867 loop : -0.42 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.032 0.002 TYR G 48 PHE 0.018 0.002 PHE F 34 TRP 0.013 0.002 TRP F 52 HIS 0.008 0.002 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00571 (19602) covalent geometry : angle 0.58580 (26637) SS BOND : bond 0.00405 ( 21) SS BOND : angle 1.45660 ( 42) hydrogen bonds : bond 0.04534 ( 735) hydrogen bonds : angle 4.98407 ( 2190) *********************** 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 259 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.637 Fit side-chains REVERT: A 568 MET cc_start: 0.7535 (mtm) cc_final: 0.7329 (ttm) REVERT: A 650 PHE cc_start: 0.6832 (m-80) cc_final: 0.6602 (m-10) REVERT: B 568 MET cc_start: 0.7987 (ptp) cc_final: 0.7320 (ptp) REVERT: B 641 PHE cc_start: 0.7840 (m-80) cc_final: 0.7635 (m-80) REVERT: C 568 MET cc_start: 0.7067 (mtp) cc_final: 0.6619 (ttm) REVERT: C 677 MET cc_start: 0.8791 (mmm) cc_final: 0.8227 (mmm) REVERT: H 67 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7391 (mtm110) REVERT: E 68 ASN cc_start: 0.8789 (m-40) cc_final: 0.8408 (m-40) REVERT: D 8 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7792 (mt0) REVERT: D 92 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7658 (mtt-85) REVERT: F 86 MET cc_start: 0.9117 (tmm) cc_final: 0.8363 (ttp) outliers start: 43 outliers final: 30 residues processed: 248 average time/residue: 0.1532 time to fit residues: 55.9344 Evaluate side-chains 235 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 347 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 529 CYS 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 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain 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 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 39 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099893 restraints weight = 29272.929| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.76 r_work: 0.3096 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19623 Z= 0.143 Angle : 0.509 13.845 26679 Z= 0.273 Chirality : 0.043 0.141 2886 Planarity : 0.004 0.043 3483 Dihedral : 4.245 22.553 2712 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.85 % Allowed : 11.18 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2397 helix: 0.75 (0.29), residues: 315 sheet: 0.66 (0.17), residues: 864 loop : -0.36 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 89 TYR 0.021 0.001 TYR G 48 PHE 0.016 0.001 PHE F 34 TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00336 (19602) covalent geometry : angle 0.50745 (26637) SS BOND : bond 0.00315 ( 21) SS BOND : angle 1.01471 ( 42) hydrogen bonds : bond 0.03920 ( 735) hydrogen bonds : angle 4.77929 ( 2190) *********************** 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 273 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8066 (t0) cc_final: 0.7841 (t0) REVERT: A 604 PHE cc_start: 0.7827 (p90) cc_final: 0.7210 (p90) REVERT: B 568 MET cc_start: 0.7942 (ptp) cc_final: 0.7290 (ptp) REVERT: C 568 MET cc_start: 0.6883 (mtp) cc_final: 0.6676 (ttm) REVERT: C 653 TYR cc_start: 0.6579 (m-80) cc_final: 0.6224 (m-80) REVERT: C 677 MET cc_start: 0.8782 (mmm) cc_final: 0.8272 (mmm) REVERT: H 67 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7397 (mtm110) REVERT: E 68 ASN cc_start: 0.8744 (m-40) cc_final: 0.8370 (m-40) REVERT: D 8 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7722 (mt0) REVERT: D 92 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7603 (mtt-85) REVERT: D 114 MET cc_start: 0.8860 (mtt) cc_final: 0.8310 (mtt) outliers start: 38 outliers final: 26 residues processed: 266 average time/residue: 0.1492 time to fit residues: 59.1143 Evaluate side-chains 238 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 501 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 135 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 676 THR 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 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 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 27 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 175 optimal weight: 0.0060 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 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 = 0.3561 r_free = 0.3561 target = 0.123635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098140 restraints weight = 29389.408| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.82 r_work: 0.3054 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19623 Z= 0.203 Angle : 0.542 14.085 26679 Z= 0.292 Chirality : 0.044 0.164 2886 Planarity : 0.004 0.043 3483 Dihedral : 4.383 22.550 2712 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.49 % Allowed : 11.57 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2397 helix: 0.59 (0.29), residues: 315 sheet: 0.53 (0.17), residues: 882 loop : -0.39 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 89 TYR 0.029 0.002 TYR E 48 PHE 0.022 0.002 PHE B 641 TRP 0.013 0.002 TRP F 52 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00488 (19602) covalent geometry : angle 0.54026 (26637) SS BOND : bond 0.00387 ( 21) SS BOND : angle 1.29297 ( 42) hydrogen bonds : bond 0.04198 ( 735) hydrogen bonds : angle 4.84331 ( 2190) *********************** 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 265 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7469 (t0) cc_final: 0.7208 (t0) REVERT: A 188 ASP cc_start: 0.8104 (t0) cc_final: 0.7863 (t0) REVERT: A 534 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.8273 (t-90) REVERT: A 604 PHE cc_start: 0.7990 (p90) cc_final: 0.7599 (p90) REVERT: A 673 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8641 (tt) REVERT: B 366 MET cc_start: 0.8524 (mmt) cc_final: 0.8180 (mmt) REVERT: B 568 MET cc_start: 0.8039 (ptp) cc_final: 0.7570 (ptp) REVERT: B 647 TYR cc_start: 0.7713 (m-80) cc_final: 0.6722 (m-80) REVERT: C 568 MET cc_start: 0.7150 (mtp) cc_final: 0.6675 (ttm) REVERT: C 653 TYR cc_start: 0.6782 (m-80) cc_final: 0.6380 (m-80) REVERT: C 677 MET cc_start: 0.8810 (mmm) cc_final: 0.8331 (mmm) REVERT: H 67 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7405 (mtm110) REVERT: E 68 ASN cc_start: 0.8801 (m-40) cc_final: 0.8438 (m-40) REVERT: D 8 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7783 (mt0) REVERT: D 92 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7729 (mtt-85) outliers start: 51 outliers final: 43 residues processed: 252 average time/residue: 0.1609 time to fit residues: 59.9519 Evaluate side-chains 250 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 170 VAL 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 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 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 E residue 12 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 12 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 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 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 223 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 193 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100010 restraints weight = 29156.981| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.75 r_work: 0.3084 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19623 Z= 0.146 Angle : 0.498 14.544 26679 Z= 0.268 Chirality : 0.043 0.142 2886 Planarity : 0.004 0.041 3483 Dihedral : 4.242 22.563 2712 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.59 % Allowed : 12.01 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.17), residues: 2397 helix: 0.75 (0.29), residues: 315 sheet: 0.72 (0.17), residues: 855 loop : -0.40 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 89 TYR 0.021 0.001 TYR E 48 PHE 0.016 0.001 PHE F 34 TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00347 (19602) covalent geometry : angle 0.49670 (26637) SS BOND : bond 0.00331 ( 21) SS BOND : angle 1.05427 ( 42) hydrogen bonds : bond 0.03878 ( 735) hydrogen bonds : angle 4.72679 ( 2190) *********************** 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 280 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7437 (t0) cc_final: 0.7171 (t0) REVERT: A 188 ASP cc_start: 0.8070 (t0) cc_final: 0.7850 (t0) REVERT: A 534 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.8148 (t-90) REVERT: A 622 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: A 673 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 230 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 366 MET cc_start: 0.8485 (mmt) cc_final: 0.8108 (mmt) REVERT: B 562 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7528 (ptm-80) REVERT: B 568 MET cc_start: 0.8015 (ptp) cc_final: 0.7286 (ptp) REVERT: B 647 TYR cc_start: 0.7713 (m-80) cc_final: 0.6857 (m-80) REVERT: C 568 MET cc_start: 0.7079 (mtp) cc_final: 0.6724 (ttm) REVERT: C 653 TYR cc_start: 0.6747 (m-80) cc_final: 0.6353 (m-80) REVERT: C 677 MET cc_start: 0.8707 (mmm) cc_final: 0.8275 (mmm) REVERT: H 67 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7425 (mtm110) REVERT: E 68 ASN cc_start: 0.8762 (m-40) cc_final: 0.8399 (m-40) REVERT: D 8 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7723 (mt0) REVERT: D 92 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7522 (mtt-85) outliers start: 53 outliers final: 44 residues processed: 268 average time/residue: 0.1471 time to fit residues: 58.1622 Evaluate side-chains 264 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 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 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 230 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 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 12 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 69 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 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 75 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 216 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 227 optimal weight: 0.0060 chunk 203 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- 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 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 = 0.3610 r_free = 0.3610 target = 0.127275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101026 restraints weight = 29192.514| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.92 r_work: 0.3100 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19623 Z= 0.097 Angle : 0.463 14.025 26679 Z= 0.249 Chirality : 0.041 0.137 2886 Planarity : 0.004 0.040 3483 Dihedral : 3.998 22.004 2712 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.81 % Allowed : 13.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2397 helix: 1.08 (0.29), residues: 315 sheet: 0.79 (0.17), residues: 864 loop : -0.27 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 89 TYR 0.014 0.001 TYR L 48 PHE 0.013 0.001 PHE F 34 TRP 0.013 0.001 TRP H 52 HIS 0.005 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00220 (19602) covalent geometry : angle 0.46243 (26637) SS BOND : bond 0.00291 ( 21) SS BOND : angle 0.85083 ( 42) hydrogen bonds : bond 0.03516 ( 735) hydrogen bonds : angle 4.53453 ( 2190) *********************** 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 277 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7508 (t0) cc_final: 0.7236 (t0) REVERT: A 136 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6711 (mtt90) REVERT: A 534 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.8078 (t-90) REVERT: B 366 MET cc_start: 0.8468 (mmt) cc_final: 0.8065 (mmt) REVERT: B 568 MET cc_start: 0.7923 (ptp) cc_final: 0.7258 (ptp) REVERT: B 647 TYR cc_start: 0.7724 (m-80) cc_final: 0.7054 (m-80) REVERT: C 653 TYR cc_start: 0.6605 (m-80) cc_final: 0.6195 (m-80) REVERT: C 677 MET cc_start: 0.8776 (mmm) cc_final: 0.8425 (mmm) REVERT: H 67 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7443 (mtm110) REVERT: G 48 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8333 (p90) REVERT: D 8 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7761 (mt0) REVERT: D 92 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7539 (mtt-85) REVERT: D 114 MET cc_start: 0.8794 (mtt) cc_final: 0.8215 (mtt) outliers start: 37 outliers final: 26 residues processed: 266 average time/residue: 0.1555 time to fit residues: 60.9084 Evaluate side-chains 248 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 373 ASP Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 576 VAL 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 347 THR Chi-restraints excluded: chain B residue 456 LEU 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 676 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 96 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 2 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 212 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.124735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099868 restraints weight = 29548.323| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.80 r_work: 0.3079 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19623 Z= 0.187 Angle : 0.527 15.017 26679 Z= 0.282 Chirality : 0.044 0.153 2886 Planarity : 0.004 0.041 3483 Dihedral : 4.231 22.244 2712 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.64 % Allowed : 13.18 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2397 helix: 0.80 (0.29), residues: 315 sheet: 0.71 (0.17), residues: 867 loop : -0.34 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 89 TYR 0.026 0.002 TYR L 48 PHE 0.022 0.002 PHE A 194 TRP 0.013 0.002 TRP F 52 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00448 (19602) covalent geometry : angle 0.52543 (26637) SS BOND : bond 0.00325 ( 21) SS BOND : angle 1.14891 ( 42) hydrogen bonds : bond 0.03986 ( 735) hydrogen bonds : angle 4.71084 ( 2190) *********************** 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 272 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7493 (t0) cc_final: 0.7209 (t0) REVERT: A 136 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6793 (mtt90) REVERT: A 375 MET cc_start: 0.8237 (mtp) cc_final: 0.7954 (mtp) REVERT: A 534 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8180 (t-90) REVERT: A 604 PHE cc_start: 0.7794 (p90) cc_final: 0.7464 (p90) REVERT: A 616 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7506 (tp-100) REVERT: A 622 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: A 624 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7035 (mtp85) REVERT: A 673 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 230 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 366 MET cc_start: 0.8488 (mmt) cc_final: 0.8065 (mmt) REVERT: B 568 MET cc_start: 0.8018 (ptp) cc_final: 0.7304 (ptp) REVERT: B 647 TYR cc_start: 0.7700 (m-80) cc_final: 0.7020 (m-80) REVERT: C 653 TYR cc_start: 0.6719 (m-80) cc_final: 0.6298 (m-80) REVERT: C 677 MET cc_start: 0.8774 (mmm) cc_final: 0.8385 (mmm) REVERT: H 34 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8377 (t80) REVERT: D 8 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7747 (mt0) REVERT: D 24 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8491 (ttm-80) REVERT: D 92 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7564 (mtt-85) outliers start: 54 outliers final: 46 residues processed: 259 average time/residue: 0.1627 time to fit residues: 61.7376 Evaluate side-chains 267 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 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 135 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 456 LEU 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 640 TYR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 118 optimal weight: 0.0870 chunk 181 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099141 restraints weight = 29152.408| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.94 r_work: 0.3075 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19623 Z= 0.134 Angle : 0.499 14.884 26679 Z= 0.267 Chirality : 0.043 0.141 2886 Planarity : 0.004 0.041 3483 Dihedral : 4.146 22.189 2712 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.39 % Allowed : 13.86 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2397 helix: 0.91 (0.29), residues: 315 sheet: 0.72 (0.17), residues: 867 loop : -0.31 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 89 TYR 0.024 0.001 TYR C 429 PHE 0.015 0.001 PHE F 34 TRP 0.012 0.001 TRP F 52 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00315 (19602) covalent geometry : angle 0.49743 (26637) SS BOND : bond 0.00295 ( 21) SS BOND : angle 1.01532 ( 42) hydrogen bonds : bond 0.03757 ( 735) hydrogen bonds : angle 4.66466 ( 2190) *********************** 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 269 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7488 (t0) cc_final: 0.7207 (t0) REVERT: A 136 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.6831 (mtt90) REVERT: A 375 MET cc_start: 0.8338 (mtp) cc_final: 0.8114 (mtp) REVERT: A 534 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8125 (t-90) REVERT: A 616 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7559 (tp-100) REVERT: A 622 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: A 624 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7013 (mtp85) REVERT: A 673 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 230 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 366 MET cc_start: 0.8489 (mmt) cc_final: 0.8063 (mmt) REVERT: B 562 ARG cc_start: 0.8049 (ptm-80) cc_final: 0.7571 (ptm160) REVERT: B 568 MET cc_start: 0.8025 (ptp) cc_final: 0.7318 (ptp) REVERT: B 647 TYR cc_start: 0.7700 (m-80) cc_final: 0.7051 (m-80) REVERT: C 653 TYR cc_start: 0.6685 (m-80) cc_final: 0.6278 (m-80) REVERT: C 677 MET cc_start: 0.8793 (mmm) cc_final: 0.8429 (mmm) REVERT: H 34 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8410 (t80) REVERT: G 59 GLU cc_start: 0.7926 (tp30) cc_final: 0.7720 (tp30) REVERT: D 8 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7780 (mt0) REVERT: D 24 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8498 (ttm-80) REVERT: D 92 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7543 (mtt-85) outliers start: 49 outliers final: 39 residues processed: 259 average time/residue: 0.1583 time to fit residues: 60.1091 Evaluate side-chains 262 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 456 LEU 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 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain 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 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 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 226 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 236 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3567 r_free = 0.3567 target = 0.124020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099180 restraints weight = 29303.796| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.69 r_work: 0.3069 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19623 Z= 0.190 Angle : 0.539 15.130 26679 Z= 0.289 Chirality : 0.044 0.169 2886 Planarity : 0.004 0.042 3483 Dihedral : 4.298 22.319 2712 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.49 % Allowed : 13.86 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2397 helix: 0.76 (0.29), residues: 315 sheet: 0.62 (0.17), residues: 867 loop : -0.38 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 89 TYR 0.026 0.002 TYR C 429 PHE 0.018 0.002 PHE F 34 TRP 0.013 0.002 TRP F 52 HIS 0.005 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00456 (19602) covalent geometry : angle 0.53547 (26637) SS BOND : bond 0.00326 ( 21) SS BOND : angle 1.60108 ( 42) hydrogen bonds : bond 0.04063 ( 735) hydrogen bonds : angle 4.75838 ( 2190) ********************** 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 270 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7435 (t0) cc_final: 0.7134 (t0) REVERT: A 136 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6853 (mtt90) REVERT: A 183 MET cc_start: 0.8641 (mmt) cc_final: 0.8245 (mmt) REVERT: A 375 MET cc_start: 0.8308 (mtp) cc_final: 0.8080 (mtp) REVERT: A 534 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8175 (t-90) REVERT: A 616 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7458 (tp-100) REVERT: A 622 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: A 624 ARG cc_start: 0.7619 (mtp85) cc_final: 0.6982 (mtp85) REVERT: A 673 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 195 GLU cc_start: 0.8322 (pp20) cc_final: 0.7891 (pp20) REVERT: B 230 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 366 MET cc_start: 0.8470 (mmt) cc_final: 0.8028 (mmt) REVERT: B 568 MET cc_start: 0.7970 (ptp) cc_final: 0.7209 (ptp) REVERT: B 647 TYR cc_start: 0.7691 (m-80) cc_final: 0.7005 (m-80) REVERT: C 653 TYR cc_start: 0.6662 (m-80) cc_final: 0.6329 (m-80) REVERT: C 677 MET cc_start: 0.8768 (mmm) cc_final: 0.8376 (mmm) REVERT: H 34 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8393 (t80) REVERT: G 59 GLU cc_start: 0.7906 (tp30) cc_final: 0.7698 (tp30) REVERT: D 8 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7711 (mt0) REVERT: D 24 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8446 (ttm-80) REVERT: D 92 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7507 (mtt-85) outliers start: 51 outliers final: 45 residues processed: 260 average time/residue: 0.1565 time to fit residues: 59.4794 Evaluate side-chains 266 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 456 LEU 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 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 36 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** C 126 GLN 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 = 0.3588 r_free = 0.3588 target = 0.125596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100879 restraints weight = 29239.627| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.72 r_work: 0.3104 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19623 Z= 0.130 Angle : 0.500 15.515 26679 Z= 0.267 Chirality : 0.042 0.150 2886 Planarity : 0.004 0.041 3483 Dihedral : 4.146 22.117 2712 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.59 % Allowed : 13.81 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2397 helix: 0.97 (0.29), residues: 315 sheet: 0.68 (0.17), residues: 867 loop : -0.32 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 89 TYR 0.023 0.001 TYR C 429 PHE 0.016 0.001 PHE B 262 TRP 0.012 0.001 TRP F 52 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00307 (19602) covalent geometry : angle 0.49899 (26637) SS BOND : bond 0.00286 ( 21) SS BOND : angle 0.99074 ( 42) hydrogen bonds : bond 0.03723 ( 735) hydrogen bonds : angle 4.64113 ( 2190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4964.89 seconds wall clock time: 85 minutes 28.40 seconds (5128.40 seconds total)