Starting phenix.real_space_refine on Wed Mar 4 23:20:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sco_25040/03_2026/7sco_25040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sco_25040/03_2026/7sco_25040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sco_25040/03_2026/7sco_25040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sco_25040/03_2026/7sco_25040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sco_25040/03_2026/7sco_25040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sco_25040/03_2026/7sco_25040.map" } resolution = 3.37 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 72 5.16 5 C 10767 2.51 5 N 2916 2.21 5 O 3375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17130 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 900 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 900 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "F" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 900 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "K" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.03, per 1000 atoms: 0.24 Number of scatterers: 17130 At special positions: 0 Unit cell: (129.95, 139.15, 151.8, 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 72 16.00 O 3375 8.00 N 2916 7.00 C 10767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS H 529 " - pdb=" SG CYS H 603 " distance=2.02 Simple disulfide: pdb=" SG CYS L 644 " - pdb=" SG CYS L 710 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 603 " distance=2.02 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 710 " distance=2.02 Simple disulfide: pdb=" SG CYS G 8 " - pdb=" SG CYS I 467 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 278 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 71 " distance=2.02 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 306 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 529 " - pdb=" SG CYS J 603 " distance=2.02 Simple disulfide: pdb=" SG CYS K 644 " - pdb=" SG CYS K 710 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 15 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 58 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 15 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 58 " " NAG C 404 " - " ASN C 129 " " NAG G 401 " - " ASN G 15 " " NAG G 402 " - " ASN G 27 " " NAG G 403 " - " ASN G 58 " " NAG G 404 " - " ASN G 129 " " NAG M 1 " - " ASN A 91 " " NAG N 1 " - " ASN C 91 " " NAG O 1 " - " ASN G 91 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 803.7 milliseconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 23.4% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.869A pdb=" N GLU A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 removed outlier: 3.529A pdb=" N GLU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 388 Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'H' and resid 569 through 572 Processing helix chain 'H' and resid 594 through 598 Processing helix chain 'L' and resid 701 through 705 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.869A pdb=" N GLU C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 removed outlier: 3.530A pdb=" N GLU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 367 through 388 Processing helix chain 'D' and resid 404 through 457 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 488 through 491 Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 569 through 572 Processing helix chain 'E' and resid 594 through 598 Processing helix chain 'F' and resid 701 through 705 Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 68 through 75 removed outlier: 3.870A pdb=" N GLU G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.529A pdb=" N GLU G 107 " --> pdb=" O GLU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 367 through 388 Processing helix chain 'I' and resid 404 through 457 Processing helix chain 'I' and resid 475 through 485 Processing helix chain 'I' and resid 488 through 491 Processing helix chain 'I' and resid 492 through 501 Processing helix chain 'I' and resid 502 through 504 No H-bonds generated for 'chain 'I' and resid 502 through 504' Processing helix chain 'J' and resid 535 through 539 Processing helix chain 'J' and resid 569 through 572 Processing helix chain 'J' and resid 594 through 598 Processing helix chain 'K' and resid 701 through 705 Processing sheet with id=AA1, first strand: chain 'B' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.511A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.452A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 289 Processing sheet with id=AB2, first strand: chain 'H' and resid 510 through 513 Processing sheet with id=AB3, first strand: chain 'H' and resid 517 through 519 removed outlier: 6.002A pdb=" N ARG H 545 " --> pdb=" O TRP H 554 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP H 554 " --> pdb=" O ARG H 545 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET H 555 " --> pdb=" O TYR H 567 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR H 567 " --> pdb=" O MET H 555 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG H 557 " --> pdb=" O GLU H 565 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU H 565 " --> pdb=" O ARG H 557 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 517 through 519 Processing sheet with id=AB5, first strand: chain 'L' and resid 625 through 626 Processing sheet with id=AB6, first strand: chain 'L' and resid 632 through 634 removed outlier: 7.003A pdb=" N LEU L 632 " --> pdb=" O GLU L 727 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 657 " --> pdb=" O LEU L 669 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 361 through 366 Processing sheet with id=AB8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.512A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 112 through 119 removed outlier: 6.747A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 112 through 119 removed outlier: 6.747A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.453A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 287 through 289 Processing sheet with id=AC8, first strand: chain 'E' and resid 510 through 513 Processing sheet with id=AC9, first strand: chain 'E' and resid 517 through 519 removed outlier: 6.002A pdb=" N ARG E 545 " --> pdb=" O TRP E 554 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP E 554 " --> pdb=" O ARG E 545 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET E 555 " --> pdb=" O TYR E 567 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR E 567 " --> pdb=" O MET E 555 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG E 557 " --> pdb=" O GLU E 565 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU E 565 " --> pdb=" O ARG E 557 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 517 through 519 Processing sheet with id=AD2, first strand: chain 'F' and resid 625 through 626 Processing sheet with id=AD3, first strand: chain 'F' and resid 632 through 634 removed outlier: 7.003A pdb=" N LEU F 632 " --> pdb=" O GLU F 727 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP F 657 " --> pdb=" O LEU F 669 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 361 through 366 Processing sheet with id=AD5, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD6, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AD7, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'G' and resid 54 through 57 removed outlier: 6.512A pdb=" N LEU G 54 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE G 83 " --> pdb=" O ILE G 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'G' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.453A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE4, first strand: chain 'G' and resid 287 through 289 Processing sheet with id=AE5, first strand: chain 'J' and resid 510 through 513 Processing sheet with id=AE6, first strand: chain 'J' and resid 517 through 519 removed outlier: 6.001A pdb=" N ARG J 545 " --> pdb=" O TRP J 554 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP J 554 " --> pdb=" O ARG J 545 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET J 555 " --> pdb=" O TYR J 567 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR J 567 " --> pdb=" O MET J 555 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG J 557 " --> pdb=" O GLU J 565 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU J 565 " --> pdb=" O ARG J 557 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 517 through 519 Processing sheet with id=AE8, first strand: chain 'K' and resid 625 through 626 Processing sheet with id=AE9, first strand: chain 'K' and resid 632 through 634 removed outlier: 7.003A pdb=" N LEU K 632 " --> pdb=" O GLU K 727 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP K 657 " --> pdb=" O LEU K 669 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 1971 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: 3.42 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3942 1.32 - 1.46: 6019 1.46 - 1.60: 7456 1.60 - 1.74: 28 1.74 - 1.88: 87 Bond restraints: 17532 Sorted by residual: bond pdb=" CB HIS G 130 " pdb=" CG HIS G 130 " ideal model delta sigma weight residual 1.497 1.351 0.146 1.40e-02 5.10e+03 1.09e+02 bond pdb=" CB HIS C 130 " pdb=" CG HIS C 130 " ideal model delta sigma weight residual 1.497 1.351 0.146 1.40e-02 5.10e+03 1.08e+02 bond pdb=" CB HIS A 130 " pdb=" CG HIS A 130 " ideal model delta sigma weight residual 1.497 1.352 0.145 1.40e-02 5.10e+03 1.08e+02 bond pdb=" CB HIS A 41 " pdb=" CG HIS A 41 " ideal model delta sigma weight residual 1.497 1.401 0.096 1.40e-02 5.10e+03 4.72e+01 bond pdb=" CB HIS C 41 " pdb=" CG HIS C 41 " ideal model delta sigma weight residual 1.497 1.401 0.096 1.40e-02 5.10e+03 4.72e+01 ... (remaining 17527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 20332 2.39 - 4.77: 2976 4.77 - 7.16: 449 7.16 - 9.54: 24 9.54 - 11.93: 3 Bond angle restraints: 23784 Sorted by residual: angle pdb=" N THR C 319 " pdb=" CA THR C 319 " pdb=" C THR C 319 " ideal model delta sigma weight residual 114.04 102.11 11.93 1.24e+00 6.50e-01 9.25e+01 angle pdb=" N THR A 319 " pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 114.04 102.12 11.92 1.24e+00 6.50e-01 9.24e+01 angle pdb=" N THR G 319 " pdb=" CA THR G 319 " pdb=" C THR G 319 " ideal model delta sigma weight residual 114.04 102.17 11.87 1.24e+00 6.50e-01 9.16e+01 angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.30e-01 1.88e+00 8.02e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.66 126.19 -6.53 7.30e-01 1.88e+00 7.99e+01 ... (remaining 23779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10360 17.88 - 35.75: 228 35.75 - 53.63: 59 53.63 - 71.51: 36 71.51 - 89.39: 9 Dihedral angle restraints: 10692 sinusoidal: 4488 harmonic: 6204 Sorted by residual: dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sinusoidal sigma weight residual -86.00 -138.99 52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS G 46 " pdb=" SG CYS G 46 " pdb=" SG CYS G 278 " pdb=" CB CYS G 278 " ideal model delta sinusoidal sigma weight residual -86.00 -138.98 52.98 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 10689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1866 0.101 - 0.203: 584 0.203 - 0.304: 106 0.304 - 0.406: 24 0.406 - 0.507: 24 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.44e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.19e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.06e+01 ... (remaining 2601 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 195 " -0.065 2.00e-02 2.50e+03 3.34e-02 2.23e+01 pdb=" CG TYR A 195 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 195 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 195 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 195 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 195 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 195 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 195 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 195 " 0.065 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" CG TYR C 195 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 195 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 195 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 195 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 195 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR C 195 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 195 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 195 " 0.065 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" CG TYR G 195 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR G 195 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR G 195 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR G 195 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR G 195 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 195 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 195 " 0.044 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 12 2.48 - 3.09: 11772 3.09 - 3.69: 25768 3.69 - 4.30: 40619 4.30 - 4.90: 65362 Nonbonded interactions: 143533 Sorted by model distance: nonbonded pdb=" OE1 GLN H 611 " pdb=" OH TYR L 671 " model vdw 1.876 3.040 nonbonded pdb=" OE1 GLN H 611 " pdb=" CZ TYR L 671 " model vdw 2.309 3.260 nonbonded pdb=" OD1 ASP B 415 " pdb=" NZ LYS I 413 " model vdw 2.370 3.120 nonbonded pdb=" NZ LYS D 413 " pdb=" OD1 ASP I 415 " model vdw 2.370 3.120 nonbonded pdb=" NZ LYS B 413 " pdb=" OD1 ASP D 415 " model vdw 2.370 3.120 ... (remaining 143528 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.450 Find NCS groups from input model: 0.300 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.021 0.163 17574 Z= 1.143 Angle : 1.745 11.926 23886 Z= 1.178 Chirality : 0.110 0.507 2604 Planarity : 0.009 0.051 3069 Dihedral : 9.571 89.386 6672 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.59 (0.17), residues: 2133 helix: 0.69 (0.22), residues: 375 sheet: 0.50 (0.20), residues: 570 loop : 0.38 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 262 TYR 0.065 0.008 TYR A 195 PHE 0.035 0.007 PHE F 705 TRP 0.038 0.009 TRP G 127 HIS 0.011 0.003 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.02121 (17532) covalent geometry : angle 1.73218 (23784) SS BOND : bond 0.00591 ( 24) SS BOND : angle 4.35114 ( 48) hydrogen bonds : bond 0.16645 ( 741) hydrogen bonds : angle 7.35889 ( 1971) link_BETA1-4 : bond 0.07248 ( 3) link_BETA1-4 : angle 4.65965 ( 9) link_NAG-ASN : bond 0.08476 ( 15) link_NAG-ASN : angle 2.47331 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 LYS cc_start: 0.7998 (mttm) cc_final: 0.7577 (mtmm) REVERT: B 412 LYS cc_start: 0.8869 (tttm) cc_final: 0.8659 (mttp) REVERT: H 555 MET cc_start: 0.8295 (mtp) cc_final: 0.8021 (mtp) REVERT: H 614 PRO cc_start: 0.7667 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: L 632 LEU cc_start: 0.5669 (tp) cc_final: 0.5388 (tp) REVERT: L 694 THR cc_start: 0.8251 (m) cc_final: 0.8017 (p) REVERT: C 208 HIS cc_start: 0.8128 (m-70) cc_final: 0.7890 (m-70) REVERT: D 402 LYS cc_start: 0.8020 (mttm) cc_final: 0.7780 (mtmm) REVERT: E 535 THR cc_start: 0.7386 (m) cc_final: 0.7035 (p) REVERT: E 614 PRO cc_start: 0.7830 (Cg_endo) cc_final: 0.7591 (Cg_exo) REVERT: F 632 LEU cc_start: 0.5559 (tp) cc_final: 0.4718 (tp) REVERT: F 687 SER cc_start: 0.7335 (p) cc_final: 0.6895 (m) REVERT: J 526 LYS cc_start: 0.7121 (tttt) cc_final: 0.6778 (ttpt) REVERT: K 687 SER cc_start: 0.7671 (p) cc_final: 0.7203 (m) REVERT: K 707 LEU cc_start: 0.6814 (mt) cc_final: 0.6604 (mp) REVERT: K 708 TYR cc_start: 0.7473 (m-80) cc_final: 0.7176 (m-80) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.1546 time to fit residues: 119.8017 Evaluate side-chains 294 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 250 ASN B 401 ASN ** L 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 510 GLN ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 208 HIS I 355 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128076 restraints weight = 26214.311| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.15 r_work: 0.3558 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17574 Z= 0.180 Angle : 0.702 9.694 23886 Z= 0.380 Chirality : 0.046 0.165 2604 Planarity : 0.005 0.053 3069 Dihedral : 5.257 24.460 2727 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.10 % Allowed : 8.24 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.37 (0.17), residues: 2133 helix: 1.47 (0.25), residues: 378 sheet: 0.43 (0.23), residues: 462 loop : -0.14 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 676 TYR 0.032 0.002 TYR G 102 PHE 0.018 0.002 PHE C 118 TRP 0.013 0.001 TRP D 351 HIS 0.018 0.002 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00388 (17532) covalent geometry : angle 0.69375 (23784) SS BOND : bond 0.00361 ( 24) SS BOND : angle 1.83614 ( 48) hydrogen bonds : bond 0.05510 ( 741) hydrogen bonds : angle 6.12812 ( 1971) link_BETA1-4 : bond 0.00184 ( 3) link_BETA1-4 : angle 1.62348 ( 9) link_NAG-ASN : bond 0.00283 ( 15) link_NAG-ASN : angle 1.76566 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 345 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7503 (mtm-85) REVERT: B 402 LYS cc_start: 0.8292 (mttm) cc_final: 0.8072 (mtmm) REVERT: B 462 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: H 614 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8252 (Cg_exo) REVERT: L 687 SER cc_start: 0.8942 (p) cc_final: 0.8438 (m) REVERT: L 694 THR cc_start: 0.8441 (m) cc_final: 0.8195 (p) REVERT: L 713 TYR cc_start: 0.8135 (p90) cc_final: 0.7802 (p90) REVERT: D 402 LYS cc_start: 0.8165 (mttm) cc_final: 0.7798 (mtmm) REVERT: D 487 TYR cc_start: 0.7133 (t80) cc_final: 0.6710 (t80) REVERT: E 584 SER cc_start: 0.8307 (m) cc_final: 0.7821 (p) REVERT: F 687 SER cc_start: 0.8552 (p) cc_final: 0.8041 (m) REVERT: G 9 ILE cc_start: 0.8752 (mt) cc_final: 0.8498 (mt) REVERT: G 301 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8654 (m) REVERT: J 526 LYS cc_start: 0.7472 (tttt) cc_final: 0.6891 (ttpt) REVERT: J 535 THR cc_start: 0.7682 (m) cc_final: 0.7202 (p) REVERT: J 584 SER cc_start: 0.8266 (m) cc_final: 0.8025 (p) REVERT: K 687 SER cc_start: 0.8454 (p) cc_final: 0.8007 (m) REVERT: K 707 LEU cc_start: 0.6684 (mt) cc_final: 0.6354 (mp) outliers start: 39 outliers final: 21 residues processed: 364 average time/residue: 0.1295 time to fit residues: 71.3234 Evaluate side-chains 303 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 355 HIS B 392 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN D 355 HIS ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN K 648 GLN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118886 restraints weight = 26889.867| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.15 r_work: 0.3431 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17574 Z= 0.247 Angle : 0.698 8.646 23886 Z= 0.369 Chirality : 0.046 0.197 2604 Planarity : 0.006 0.069 3069 Dihedral : 5.115 31.056 2727 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.18 % Allowed : 9.53 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.01 (0.17), residues: 2133 helix: 1.28 (0.25), residues: 378 sheet: 0.36 (0.24), residues: 456 loop : -0.52 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 725 TYR 0.022 0.003 TYR A 102 PHE 0.026 0.002 PHE B 440 TRP 0.020 0.002 TRP C 153 HIS 0.011 0.002 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00566 (17532) covalent geometry : angle 0.68796 (23784) SS BOND : bond 0.00452 ( 24) SS BOND : angle 2.03076 ( 48) hydrogen bonds : bond 0.05046 ( 741) hydrogen bonds : angle 6.01128 ( 1971) link_BETA1-4 : bond 0.00078 ( 3) link_BETA1-4 : angle 1.66502 ( 9) link_NAG-ASN : bond 0.00469 ( 15) link_NAG-ASN : angle 1.92707 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7033 (mtm-85) REVERT: A 301 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8716 (m) REVERT: B 402 LYS cc_start: 0.8544 (mttm) cc_final: 0.8265 (mtmm) REVERT: H 524 SER cc_start: 0.7572 (p) cc_final: 0.7138 (t) REVERT: H 526 LYS cc_start: 0.7522 (tttt) cc_final: 0.7053 (ttpt) REVERT: H 553 GLU cc_start: 0.7195 (tt0) cc_final: 0.6737 (mt-10) REVERT: H 584 SER cc_start: 0.8633 (m) cc_final: 0.8275 (p) REVERT: H 600 VAL cc_start: 0.7054 (OUTLIER) cc_final: 0.6810 (p) REVERT: L 655 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8810 (tp) REVERT: L 687 SER cc_start: 0.9064 (p) cc_final: 0.8654 (m) REVERT: L 692 ASP cc_start: 0.5589 (t0) cc_final: 0.5165 (p0) REVERT: L 694 THR cc_start: 0.8638 (m) cc_final: 0.8278 (p) REVERT: L 713 TYR cc_start: 0.8296 (p90) cc_final: 0.8023 (p90) REVERT: C 25 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: C 276 ASP cc_start: 0.7316 (m-30) cc_final: 0.6994 (p0) REVERT: D 347 MET cc_start: 0.8422 (ttp) cc_final: 0.8207 (ttp) REVERT: D 402 LYS cc_start: 0.8373 (mttm) cc_final: 0.8149 (mtmm) REVERT: E 584 SER cc_start: 0.8587 (m) cc_final: 0.8115 (p) REVERT: E 600 VAL cc_start: 0.6893 (t) cc_final: 0.6641 (p) REVERT: F 687 SER cc_start: 0.8805 (p) cc_final: 0.8321 (m) REVERT: F 692 ASP cc_start: 0.5494 (t0) cc_final: 0.4837 (p0) REVERT: G 25 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: G 301 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8709 (m) REVERT: I 439 ASP cc_start: 0.7562 (t0) cc_final: 0.7356 (m-30) REVERT: I 469 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7812 (mm-30) REVERT: J 526 LYS cc_start: 0.7438 (tttt) cc_final: 0.6845 (ttpt) REVERT: J 584 SER cc_start: 0.8565 (m) cc_final: 0.8305 (p) REVERT: K 687 SER cc_start: 0.8741 (p) cc_final: 0.8256 (m) REVERT: K 692 ASP cc_start: 0.5568 (t0) cc_final: 0.4992 (p0) outliers start: 59 outliers final: 43 residues processed: 340 average time/residue: 0.1201 time to fit residues: 63.4580 Evaluate side-chains 321 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 655 LEU Chi-restraints excluded: chain L residue 696 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 360 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122652 restraints weight = 26534.847| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.15 r_work: 0.3489 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17574 Z= 0.121 Angle : 0.583 8.795 23886 Z= 0.305 Chirality : 0.042 0.162 2604 Planarity : 0.005 0.058 3069 Dihedral : 4.711 32.139 2727 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.15 % Allowed : 11.63 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.08 (0.18), residues: 2133 helix: 1.43 (0.26), residues: 381 sheet: 0.01 (0.23), residues: 498 loop : -0.30 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 574 TYR 0.023 0.002 TYR K 713 PHE 0.016 0.002 PHE C 118 TRP 0.007 0.001 TRP G 180 HIS 0.009 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00258 (17532) covalent geometry : angle 0.57327 (23784) SS BOND : bond 0.00475 ( 24) SS BOND : angle 1.92984 ( 48) hydrogen bonds : bond 0.04339 ( 741) hydrogen bonds : angle 5.71726 ( 1971) link_BETA1-4 : bond 0.00253 ( 3) link_BETA1-4 : angle 1.41627 ( 9) link_NAG-ASN : bond 0.00244 ( 15) link_NAG-ASN : angle 1.60163 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6925 (mtm-85) REVERT: B 389 MET cc_start: 0.8817 (tpt) cc_final: 0.8530 (tpt) REVERT: B 402 LYS cc_start: 0.8326 (mttm) cc_final: 0.8112 (mtmm) REVERT: H 584 SER cc_start: 0.8600 (m) cc_final: 0.8283 (p) REVERT: H 600 VAL cc_start: 0.6920 (t) cc_final: 0.6673 (p) REVERT: L 687 SER cc_start: 0.9176 (p) cc_final: 0.8716 (m) REVERT: L 692 ASP cc_start: 0.5461 (t0) cc_final: 0.5168 (p0) REVERT: L 694 THR cc_start: 0.8605 (m) cc_final: 0.8304 (p) REVERT: L 713 TYR cc_start: 0.8341 (p90) cc_final: 0.8023 (p90) REVERT: C 25 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: E 524 SER cc_start: 0.6930 (p) cc_final: 0.6723 (t) REVERT: E 539 TYR cc_start: 0.8401 (m-80) cc_final: 0.8031 (m-80) REVERT: E 584 SER cc_start: 0.8619 (m) cc_final: 0.8141 (p) REVERT: E 600 VAL cc_start: 0.6805 (t) cc_final: 0.6507 (p) REVERT: F 638 GLU cc_start: 0.5961 (pt0) cc_final: 0.5625 (pt0) REVERT: F 687 SER cc_start: 0.8759 (p) cc_final: 0.8280 (m) REVERT: F 692 ASP cc_start: 0.5412 (t0) cc_final: 0.4902 (p0) REVERT: G 25 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: G 173 GLU cc_start: 0.7364 (tp30) cc_final: 0.7081 (tp30) REVERT: G 255 TRP cc_start: 0.7567 (t60) cc_final: 0.7208 (t60) REVERT: G 301 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8707 (m) REVERT: I 469 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8035 (mm-30) REVERT: J 526 LYS cc_start: 0.7589 (tttt) cc_final: 0.6976 (ttpt) REVERT: J 584 SER cc_start: 0.8428 (m) cc_final: 0.8204 (p) REVERT: K 687 SER cc_start: 0.8666 (p) cc_final: 0.8269 (m) REVERT: K 692 ASP cc_start: 0.5384 (t0) cc_final: 0.4952 (p0) outliers start: 40 outliers final: 29 residues processed: 315 average time/residue: 0.1249 time to fit residues: 60.9794 Evaluate side-chains 301 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 591 SER Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN B 383 ASN C 141 HIS ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 392 GLN I 401 ASN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113855 restraints weight = 27175.978| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.24 r_work: 0.3359 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 17574 Z= 0.337 Angle : 0.769 9.238 23886 Z= 0.397 Chirality : 0.048 0.167 2604 Planarity : 0.006 0.082 3069 Dihedral : 5.370 40.466 2727 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.93 % Allowed : 11.52 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.46 (0.17), residues: 2133 helix: 1.07 (0.25), residues: 381 sheet: -0.27 (0.21), residues: 552 loop : -0.75 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 406 TYR 0.025 0.003 TYR E 567 PHE 0.031 0.003 PHE D 440 TRP 0.024 0.003 TRP C 153 HIS 0.012 0.002 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00790 (17532) covalent geometry : angle 0.75797 (23784) SS BOND : bond 0.00876 ( 24) SS BOND : angle 2.10430 ( 48) hydrogen bonds : bond 0.05052 ( 741) hydrogen bonds : angle 6.11391 ( 1971) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 1.80191 ( 9) link_NAG-ASN : bond 0.00703 ( 15) link_NAG-ASN : angle 2.26430 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (m) REVERT: B 389 MET cc_start: 0.8802 (tpt) cc_final: 0.8457 (tpt) REVERT: B 402 LYS cc_start: 0.8382 (mttm) cc_final: 0.8149 (mtmm) REVERT: B 471 TYR cc_start: 0.6727 (m-80) cc_final: 0.6463 (m-80) REVERT: H 526 LYS cc_start: 0.7543 (tttt) cc_final: 0.7079 (ttpt) REVERT: H 584 SER cc_start: 0.8607 (m) cc_final: 0.8251 (p) REVERT: H 600 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6656 (p) REVERT: L 687 SER cc_start: 0.9283 (p) cc_final: 0.8817 (m) REVERT: L 692 ASP cc_start: 0.5995 (t0) cc_final: 0.5507 (p0) REVERT: C 25 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: E 539 TYR cc_start: 0.8594 (m-80) cc_final: 0.8201 (m-80) REVERT: E 584 SER cc_start: 0.8725 (m) cc_final: 0.8245 (p) REVERT: F 687 SER cc_start: 0.9040 (p) cc_final: 0.8631 (m) REVERT: F 692 ASP cc_start: 0.6108 (t0) cc_final: 0.5442 (p0) REVERT: G 25 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: I 469 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8007 (mm-30) REVERT: J 526 LYS cc_start: 0.7472 (tttt) cc_final: 0.6721 (ttpp) REVERT: J 584 SER cc_start: 0.8686 (m) cc_final: 0.8345 (p) REVERT: K 687 SER cc_start: 0.8943 (p) cc_final: 0.8535 (m) outliers start: 73 outliers final: 57 residues processed: 328 average time/residue: 0.1181 time to fit residues: 60.4154 Evaluate side-chains 327 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 591 SER Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 696 THR Chi-restraints excluded: chain L residue 707 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Chi-restraints excluded: chain K residue 707 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 121 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117545 restraints weight = 26818.662| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.15 r_work: 0.3418 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17574 Z= 0.151 Angle : 0.616 7.884 23886 Z= 0.319 Chirality : 0.043 0.233 2604 Planarity : 0.005 0.062 3069 Dihedral : 4.959 38.662 2727 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.69 % Allowed : 13.89 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.18), residues: 2133 helix: 1.34 (0.26), residues: 381 sheet: -0.23 (0.22), residues: 549 loop : -0.66 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 725 TYR 0.033 0.002 TYR L 713 PHE 0.015 0.002 PHE I 468 TRP 0.008 0.001 TRP G 180 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00338 (17532) covalent geometry : angle 0.60171 (23784) SS BOND : bond 0.00497 ( 24) SS BOND : angle 2.28695 ( 48) hydrogen bonds : bond 0.04257 ( 741) hydrogen bonds : angle 5.75485 ( 1971) link_BETA1-4 : bond 0.00118 ( 3) link_BETA1-4 : angle 1.61296 ( 9) link_NAG-ASN : bond 0.00339 ( 15) link_NAG-ASN : angle 2.06586 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6900 (mtm-85) REVERT: A 301 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8619 (m) REVERT: B 471 TYR cc_start: 0.6716 (m-80) cc_final: 0.6515 (m-80) REVERT: H 584 SER cc_start: 0.8632 (m) cc_final: 0.8298 (p) REVERT: H 600 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6663 (p) REVERT: L 634 LEU cc_start: 0.8062 (mm) cc_final: 0.7610 (mt) REVERT: L 687 SER cc_start: 0.9199 (p) cc_final: 0.8817 (m) REVERT: L 692 ASP cc_start: 0.6028 (t0) cc_final: 0.5582 (p0) REVERT: C 25 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: C 276 ASP cc_start: 0.7648 (m-30) cc_final: 0.7353 (m-30) REVERT: C 286 GLN cc_start: 0.7870 (mt0) cc_final: 0.7535 (mt0) REVERT: E 539 TYR cc_start: 0.8484 (m-80) cc_final: 0.8107 (m-80) REVERT: E 584 SER cc_start: 0.8672 (m) cc_final: 0.8262 (p) REVERT: F 687 SER cc_start: 0.8927 (p) cc_final: 0.8555 (m) REVERT: F 692 ASP cc_start: 0.5958 (t0) cc_final: 0.5329 (p0) REVERT: G 120 ILE cc_start: 0.8355 (tt) cc_final: 0.8150 (tt) REVERT: I 469 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8252 (mm-30) REVERT: J 584 SER cc_start: 0.8520 (m) cc_final: 0.8255 (p) REVERT: K 687 SER cc_start: 0.8937 (p) cc_final: 0.8503 (m) REVERT: K 692 ASP cc_start: 0.5815 (t0) cc_final: 0.5322 (p0) outliers start: 50 outliers final: 39 residues processed: 301 average time/residue: 0.1224 time to fit residues: 57.2121 Evaluate side-chains 304 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 607 SER Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 141 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 178 optimal weight: 0.0770 chunk 100 optimal weight: 6.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118678 restraints weight = 26691.329| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.14 r_work: 0.3430 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17574 Z= 0.133 Angle : 0.589 9.891 23886 Z= 0.302 Chirality : 0.042 0.212 2604 Planarity : 0.005 0.060 3069 Dihedral : 4.769 37.049 2727 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.58 % Allowed : 14.22 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.18 (0.18), residues: 2133 helix: 1.47 (0.26), residues: 381 sheet: -0.12 (0.22), residues: 534 loop : -0.60 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 725 TYR 0.031 0.001 TYR L 713 PHE 0.014 0.001 PHE I 440 TRP 0.006 0.001 TRP A 64 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00300 (17532) covalent geometry : angle 0.57553 (23784) SS BOND : bond 0.00526 ( 24) SS BOND : angle 2.21627 ( 48) hydrogen bonds : bond 0.04061 ( 741) hydrogen bonds : angle 5.62735 ( 1971) link_BETA1-4 : bond 0.00203 ( 3) link_BETA1-4 : angle 1.42144 ( 9) link_NAG-ASN : bond 0.00271 ( 15) link_NAG-ASN : angle 1.81334 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6811 (mtm-85) REVERT: A 301 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8586 (m) REVERT: H 584 SER cc_start: 0.8631 (m) cc_final: 0.8302 (p) REVERT: H 600 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6697 (p) REVERT: L 634 LEU cc_start: 0.8100 (mm) cc_final: 0.7629 (mt) REVERT: L 687 SER cc_start: 0.9185 (p) cc_final: 0.8805 (m) REVERT: L 692 ASP cc_start: 0.5962 (t0) cc_final: 0.5552 (p0) REVERT: C 199 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7501 (p0) REVERT: C 275 MET cc_start: 0.6793 (tpt) cc_final: 0.6472 (tpt) REVERT: C 286 GLN cc_start: 0.7843 (mt0) cc_final: 0.7487 (mt0) REVERT: E 539 TYR cc_start: 0.8458 (m-80) cc_final: 0.8164 (m-80) REVERT: E 584 SER cc_start: 0.8560 (m) cc_final: 0.8257 (p) REVERT: F 687 SER cc_start: 0.8729 (p) cc_final: 0.8337 (m) REVERT: F 692 ASP cc_start: 0.5938 (t0) cc_final: 0.5336 (p0) REVERT: G 120 ILE cc_start: 0.8364 (tt) cc_final: 0.8145 (tt) REVERT: G 173 GLU cc_start: 0.7421 (tp30) cc_final: 0.7185 (tp30) REVERT: I 469 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8234 (mm-30) REVERT: K 687 SER cc_start: 0.8924 (p) cc_final: 0.8496 (m) REVERT: K 692 ASP cc_start: 0.5797 (t0) cc_final: 0.5322 (p0) outliers start: 48 outliers final: 37 residues processed: 295 average time/residue: 0.1219 time to fit residues: 55.8769 Evaluate side-chains 302 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 392 GLN Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 0.0570 chunk 129 optimal weight: 0.0050 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 392 GLN ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118529 restraints weight = 26755.160| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.16 r_work: 0.3428 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17574 Z= 0.136 Angle : 0.593 10.109 23886 Z= 0.305 Chirality : 0.042 0.175 2604 Planarity : 0.005 0.058 3069 Dihedral : 4.705 37.065 2727 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.75 % Allowed : 14.11 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.15 (0.18), residues: 2133 helix: 1.58 (0.26), residues: 381 sheet: -0.08 (0.22), residues: 546 loop : -0.63 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 683 TYR 0.031 0.002 TYR L 713 PHE 0.015 0.001 PHE I 440 TRP 0.007 0.001 TRP G 153 HIS 0.005 0.001 HIS I 472 Details of bonding type rmsd covalent geometry : bond 0.00307 (17532) covalent geometry : angle 0.58066 (23784) SS BOND : bond 0.00421 ( 24) SS BOND : angle 2.22063 ( 48) hydrogen bonds : bond 0.04018 ( 741) hydrogen bonds : angle 5.57392 ( 1971) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 1.29956 ( 9) link_NAG-ASN : bond 0.00281 ( 15) link_NAG-ASN : angle 1.72027 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7304 (tp30) cc_final: 0.7069 (tp30) REVERT: A 262 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6884 (mtm-85) REVERT: H 584 SER cc_start: 0.8639 (m) cc_final: 0.8323 (p) REVERT: H 600 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6683 (p) REVERT: H 614 PRO cc_start: 0.8406 (Cg_endo) cc_final: 0.8139 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7610 (mt) REVERT: L 687 SER cc_start: 0.9117 (p) cc_final: 0.8770 (m) REVERT: L 692 ASP cc_start: 0.5961 (t0) cc_final: 0.5551 (p0) REVERT: C 25 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: C 199 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7852 (p0) REVERT: C 286 GLN cc_start: 0.7781 (mt0) cc_final: 0.7403 (mt0) REVERT: D 347 MET cc_start: 0.8545 (ttm) cc_final: 0.8342 (ttm) REVERT: E 539 TYR cc_start: 0.8456 (m-80) cc_final: 0.8195 (m-80) REVERT: E 584 SER cc_start: 0.8514 (m) cc_final: 0.8260 (p) REVERT: F 687 SER cc_start: 0.8722 (p) cc_final: 0.8344 (m) REVERT: F 692 ASP cc_start: 0.5937 (t0) cc_final: 0.5318 (p0) REVERT: G 173 GLU cc_start: 0.7357 (tp30) cc_final: 0.7110 (tp30) REVERT: I 469 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8132 (mm-30) REVERT: I 498 LEU cc_start: 0.8327 (pp) cc_final: 0.7836 (mt) REVERT: K 632 LEU cc_start: 0.6680 (tp) cc_final: 0.6368 (mp) REVERT: K 634 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7645 (mt) REVERT: K 687 SER cc_start: 0.8993 (p) cc_final: 0.8479 (m) REVERT: K 692 ASP cc_start: 0.5818 (t0) cc_final: 0.5319 (p0) outliers start: 51 outliers final: 43 residues processed: 299 average time/residue: 0.1181 time to fit residues: 55.4962 Evaluate side-chains 310 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 478 CYS Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 392 GLN ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117648 restraints weight = 26846.934| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.14 r_work: 0.3416 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17574 Z= 0.153 Angle : 0.593 9.871 23886 Z= 0.305 Chirality : 0.043 0.154 2604 Planarity : 0.005 0.047 3069 Dihedral : 4.692 37.709 2727 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.34 % Allowed : 13.57 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.13 (0.18), residues: 2133 helix: 1.60 (0.26), residues: 381 sheet: -0.04 (0.23), residues: 546 loop : -0.64 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 683 TYR 0.024 0.002 TYR L 713 PHE 0.016 0.002 PHE I 440 TRP 0.009 0.001 TRP G 255 HIS 0.006 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00352 (17532) covalent geometry : angle 0.58100 (23784) SS BOND : bond 0.00468 ( 24) SS BOND : angle 2.16480 ( 48) hydrogen bonds : bond 0.04042 ( 741) hydrogen bonds : angle 5.56005 ( 1971) link_BETA1-4 : bond 0.00047 ( 3) link_BETA1-4 : angle 1.31764 ( 9) link_NAG-ASN : bond 0.00316 ( 15) link_NAG-ASN : angle 1.70502 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6824 (mtm-85) REVERT: H 584 SER cc_start: 0.8635 (m) cc_final: 0.8319 (p) REVERT: H 600 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6696 (p) REVERT: H 614 PRO cc_start: 0.8539 (Cg_endo) cc_final: 0.8249 (Cg_exo) REVERT: L 634 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7470 (mt) REVERT: L 687 SER cc_start: 0.9033 (p) cc_final: 0.8713 (m) REVERT: L 692 ASP cc_start: 0.6079 (t0) cc_final: 0.5663 (p0) REVERT: C 25 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: C 199 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (p0) REVERT: C 279 ASP cc_start: 0.6776 (t0) cc_final: 0.6366 (p0) REVERT: C 286 GLN cc_start: 0.7879 (mt0) cc_final: 0.7459 (mt0) REVERT: E 584 SER cc_start: 0.8472 (m) cc_final: 0.8257 (p) REVERT: E 614 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8223 (Cg_exo) REVERT: F 687 SER cc_start: 0.8726 (p) cc_final: 0.8388 (m) REVERT: F 692 ASP cc_start: 0.6020 (t0) cc_final: 0.5372 (p0) REVERT: G 271 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7423 (m) REVERT: I 469 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8155 (mm-30) REVERT: I 498 LEU cc_start: 0.8331 (pp) cc_final: 0.7807 (mt) REVERT: K 632 LEU cc_start: 0.6725 (tp) cc_final: 0.6387 (mp) REVERT: K 634 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7879 (mt) REVERT: K 687 SER cc_start: 0.8894 (p) cc_final: 0.8364 (m) REVERT: K 692 ASP cc_start: 0.5839 (t0) cc_final: 0.5376 (p0) outliers start: 62 outliers final: 51 residues processed: 305 average time/residue: 0.1173 time to fit residues: 56.2067 Evaluate side-chains 316 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 591 SER Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 478 CYS Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 647 SER Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 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 = 0.3850 r_free = 0.3850 target = 0.141832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117237 restraints weight = 26658.203| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.14 r_work: 0.3410 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17574 Z= 0.166 Angle : 0.608 10.004 23886 Z= 0.315 Chirality : 0.043 0.223 2604 Planarity : 0.005 0.073 3069 Dihedral : 4.733 37.470 2727 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.07 % Allowed : 14.00 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.15 (0.18), residues: 2133 helix: 1.61 (0.26), residues: 381 sheet: -0.04 (0.23), residues: 546 loop : -0.66 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 725 TYR 0.020 0.002 TYR L 713 PHE 0.017 0.002 PHE I 440 TRP 0.011 0.001 TRP C 153 HIS 0.006 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00385 (17532) covalent geometry : angle 0.59745 (23784) SS BOND : bond 0.00490 ( 24) SS BOND : angle 2.02770 ( 48) hydrogen bonds : bond 0.04069 ( 741) hydrogen bonds : angle 5.57698 ( 1971) link_BETA1-4 : bond 0.00073 ( 3) link_BETA1-4 : angle 1.33894 ( 9) link_NAG-ASN : bond 0.00327 ( 15) link_NAG-ASN : angle 1.73400 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6815 (mtm-85) REVERT: H 584 SER cc_start: 0.8669 (m) cc_final: 0.8359 (p) REVERT: H 600 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6700 (p) REVERT: H 614 PRO cc_start: 0.8545 (Cg_endo) cc_final: 0.8236 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7483 (mt) REVERT: L 687 SER cc_start: 0.9022 (p) cc_final: 0.8705 (m) REVERT: L 692 ASP cc_start: 0.6147 (t0) cc_final: 0.5726 (p0) REVERT: C 25 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: C 199 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7964 (p0) REVERT: C 279 ASP cc_start: 0.6337 (t0) cc_final: 0.5892 (p0) REVERT: C 286 GLN cc_start: 0.7950 (mt0) cc_final: 0.7563 (mt0) REVERT: E 584 SER cc_start: 0.8513 (m) cc_final: 0.8283 (p) REVERT: F 687 SER cc_start: 0.8823 (p) cc_final: 0.8413 (m) REVERT: F 692 ASP cc_start: 0.6169 (t0) cc_final: 0.5556 (p0) REVERT: G 271 SER cc_start: 0.7699 (OUTLIER) cc_final: 0.7439 (m) REVERT: G 279 ASP cc_start: 0.6451 (t0) cc_final: 0.6113 (p0) REVERT: I 469 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8161 (mm-30) REVERT: I 498 LEU cc_start: 0.8347 (pp) cc_final: 0.7814 (mt) REVERT: K 632 LEU cc_start: 0.6738 (tp) cc_final: 0.6420 (mp) REVERT: K 687 SER cc_start: 0.8904 (p) cc_final: 0.8354 (m) REVERT: K 692 ASP cc_start: 0.5874 (t0) cc_final: 0.5410 (p0) outliers start: 57 outliers final: 50 residues processed: 296 average time/residue: 0.1173 time to fit residues: 54.7108 Evaluate side-chains 311 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 478 CYS Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 201 optimal weight: 0.0070 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 123 optimal weight: 0.0470 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 0.0570 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121404 restraints weight = 26741.710| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.14 r_work: 0.3470 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17574 Z= 0.104 Angle : 0.560 10.048 23886 Z= 0.287 Chirality : 0.042 0.148 2604 Planarity : 0.004 0.063 3069 Dihedral : 4.477 35.539 2727 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.94 % Allowed : 15.29 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.00 (0.18), residues: 2133 helix: 1.76 (0.26), residues: 381 sheet: 0.03 (0.22), residues: 558 loop : -0.57 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 683 TYR 0.019 0.001 TYR L 713 PHE 0.012 0.001 PHE G 121 TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00224 (17532) covalent geometry : angle 0.55080 (23784) SS BOND : bond 0.00415 ( 24) SS BOND : angle 1.83810 ( 48) hydrogen bonds : bond 0.03725 ( 741) hydrogen bonds : angle 5.39803 ( 1971) link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 1.18253 ( 9) link_NAG-ASN : bond 0.00187 ( 15) link_NAG-ASN : angle 1.51052 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4465.15 seconds wall clock time: 77 minutes 11.09 seconds (4631.09 seconds total)