Starting phenix.real_space_refine on Sat Jul 4 00:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sco_25040/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.map" model { file = "/net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sco_25040/07_2026/7sco_25040.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 4.42, per 1000 atoms: 0.26 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: 1.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.95 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: 4.35 Time building geometry restraints manager: 2.21 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: 9985 17.88 - 35.75: 225 35.75 - 53.63: 59 53.63 - 71.51: 36 71.51 - 89.39: 9 Dihedral angle restraints: 10314 sinusoidal: 4110 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 10311 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: 0.04 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.990 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 9.757 89.386 6294 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/Z covalent geometry : bond 0.02121 / 1.14 (17532) covalent geometry : angle 1.73218 / 1.18 (23784) SS BOND : bond 0.00591 / 0.34 ( 24) SS BOND : angle 4.35114 / 2.96 ( 48) hydrogen bonds : bond 0.16645 / 10.71 ( 741) hydrogen bonds : angle 7.35889 / 5.11 ( 1971) link_BETA1-4 : bond 0.07248 / 3.63 ( 3) link_BETA1-4 : angle 4.65965 / 2.08 ( 9) link_NAG-ASN : bond 0.08476 / 5.23 ( 15) link_NAG-ASN : angle 2.47331 / 1.65 ( 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 : 0.668 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: 0.1651 time to fit residues: 129.0905 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 : 0.742 ------------------------------------------------------------------------------- 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... A 32 HIS A 250 ASN B 401 ASN ** L 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS 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 = 0.152660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128002 restraints weight = 26232.094| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.17 r_work: 0.3555 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17574 Z= 0.184 Angle : 0.702 9.374 23886 Z= 0.382 Chirality : 0.046 0.196 2604 Planarity : 0.005 0.053 3069 Dihedral : 5.122 24.170 2349 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.15 % Allowed : 8.24 % Favored : 89.61 % 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: 0.38 (0.17), residues: 2133 helix: 1.48 (0.25), residues: 378 sheet: 0.45 (0.23), residues: 462 loop : -0.14 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 676 TYR 0.031 0.002 TYR G 102 PHE 0.019 0.002 PHE C 118 TRP 0.012 0.001 TRP D 351 HIS 0.016 0.002 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (17532) covalent geometry : angle 0.69213 / 0.38 (23784) SS BOND : bond 0.01203 / 0.85 ( 24) SS BOND : angle 1.99070 / 1.35 ( 48) hydrogen bonds : bond 0.05526 / 3.53 ( 741) hydrogen bonds : angle 6.10718 / 4.24 ( 1971) link_BETA1-4 : bond 0.00384 / 0.20 ( 3) link_BETA1-4 : angle 1.56908 / 1.10 ( 9) link_NAG-ASN : bond 0.00320 / 0.21 ( 15) link_NAG-ASN : angle 1.84963 / 1.22 ( 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: 40 poor density : 344 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7527 (mtm-85) REVERT: B 389 MET cc_start: 0.9073 (mmm) cc_final: 0.8868 (tpt) REVERT: B 402 LYS cc_start: 0.8294 (mttm) cc_final: 0.8069 (mtmm) REVERT: B 462 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: H 614 PRO cc_start: 0.8521 (Cg_endo) cc_final: 0.8275 (Cg_exo) REVERT: L 687 SER cc_start: 0.8932 (p) cc_final: 0.8432 (m) REVERT: L 694 THR cc_start: 0.8452 (m) cc_final: 0.8208 (p) REVERT: L 713 TYR cc_start: 0.8132 (p90) cc_final: 0.7808 (p90) REVERT: D 402 LYS cc_start: 0.8236 (mttm) cc_final: 0.7845 (mtmm) REVERT: D 487 TYR cc_start: 0.7159 (t80) cc_final: 0.6796 (t80) REVERT: E 584 SER cc_start: 0.8297 (m) cc_final: 0.7812 (p) REVERT: F 687 SER cc_start: 0.8552 (p) cc_final: 0.8040 (m) REVERT: G 9 ILE cc_start: 0.8760 (mt) cc_final: 0.8513 (mt) REVERT: G 255 TRP cc_start: 0.7433 (t60) cc_final: 0.7231 (t60) REVERT: G 301 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (m) REVERT: J 526 LYS cc_start: 0.7469 (tttt) cc_final: 0.6890 (ttpt) REVERT: J 535 THR cc_start: 0.7682 (m) cc_final: 0.7197 (p) REVERT: J 584 SER cc_start: 0.8258 (m) cc_final: 0.8025 (p) REVERT: K 687 SER cc_start: 0.8459 (p) cc_final: 0.8010 (m) REVERT: K 707 LEU cc_start: 0.6677 (mt) cc_final: 0.6331 (mp) outliers start: 40 outliers final: 21 residues processed: 364 average time/residue: 0.1399 time to fit residues: 77.4173 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 : 0.692 ------------------------------------------------------------------------------- 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 L residue 641 THR 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: 4.9990 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS B 355 HIS B 392 GLN C 141 HIS C 272 ASN D 355 HIS G 141 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117771 restraints weight = 27002.270| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.20 r_work: 0.3413 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17574 Z= 0.285 Angle : 0.739 8.161 23886 Z= 0.389 Chirality : 0.048 0.249 2604 Planarity : 0.006 0.071 3069 Dihedral : 5.161 28.808 2349 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.39 % Allowed : 9.48 % Favored : 87.13 % 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: -0.10 (0.17), residues: 2133 helix: 1.24 (0.25), residues: 375 sheet: 0.15 (0.21), residues: 537 loop : -0.55 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 725 TYR 0.023 0.003 TYR G 11 PHE 0.028 0.003 PHE B 440 TRP 0.016 0.002 TRP G 153 HIS 0.013 0.002 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 (17532) covalent geometry : angle 0.72759 / 0.39 (23784) SS BOND : bond 0.00584 / 0.42 ( 24) SS BOND : angle 2.14362 / 1.52 ( 48) hydrogen bonds : bond 0.05190 / 3.34 ( 741) hydrogen bonds : angle 6.09327 / 4.19 ( 1971) link_BETA1-4 : bond 0.00271 / 0.14 ( 3) link_BETA1-4 : angle 1.74249 / 1.07 ( 9) link_NAG-ASN : bond 0.00602 / 0.38 ( 15) link_NAG-ASN : angle 2.11610 / 1.35 ( 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 375 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8744 (m) REVERT: B 389 MET cc_start: 0.9074 (mmm) cc_final: 0.8818 (tpt) REVERT: B 402 LYS cc_start: 0.8520 (mttm) cc_final: 0.8252 (mtmm) REVERT: H 524 SER cc_start: 0.7614 (p) cc_final: 0.7186 (t) REVERT: H 526 LYS cc_start: 0.7544 (tttt) cc_final: 0.7068 (ttpt) REVERT: H 553 GLU cc_start: 0.7266 (tt0) cc_final: 0.6843 (mt-10) REVERT: H 584 SER cc_start: 0.8633 (m) cc_final: 0.8277 (p) REVERT: H 600 VAL cc_start: 0.7099 (OUTLIER) cc_final: 0.6863 (p) REVERT: L 655 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8807 (tp) REVERT: L 687 SER cc_start: 0.9122 (p) cc_final: 0.8762 (m) REVERT: L 692 ASP cc_start: 0.5675 (t0) cc_final: 0.5234 (p0) REVERT: L 694 THR cc_start: 0.8639 (m) cc_final: 0.8267 (p) REVERT: L 713 TYR cc_start: 0.8317 (p90) cc_final: 0.8040 (p90) REVERT: C 25 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: C 276 ASP cc_start: 0.7365 (m-30) cc_final: 0.7020 (p0) REVERT: D 402 LYS cc_start: 0.8423 (mttm) cc_final: 0.8182 (mtmm) REVERT: E 584 SER cc_start: 0.8594 (m) cc_final: 0.8141 (p) REVERT: E 610 TYR cc_start: 0.8646 (m-80) cc_final: 0.8382 (m-80) REVERT: F 687 SER cc_start: 0.8862 (p) cc_final: 0.8383 (m) REVERT: F 692 ASP cc_start: 0.5629 (t0) cc_final: 0.5013 (p0) REVERT: G 25 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: G 173 GLU cc_start: 0.7509 (tp30) cc_final: 0.7308 (tp30) REVERT: G 301 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8704 (m) REVERT: I 469 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7781 (mm-30) REVERT: J 526 LYS cc_start: 0.7450 (tttt) cc_final: 0.6844 (ttpt) REVERT: J 584 SER cc_start: 0.8610 (m) cc_final: 0.8318 (p) REVERT: K 687 SER cc_start: 0.8773 (p) cc_final: 0.8300 (m) REVERT: K 692 ASP cc_start: 0.5654 (t0) cc_final: 0.5060 (p0) outliers start: 63 outliers final: 47 residues processed: 349 average time/residue: 0.1282 time to fit residues: 70.2442 Evaluate side-chains 333 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 199 ASN Chi-restraints excluded: chain A residue 250 ASN 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 591 SER 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 202 VAL 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 E residue 518 VAL Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 675 SER Chi-restraints excluded: chain G residue 25 GLU 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 368 GLN 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: 0.7980 chunk 82 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN B 360 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** 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 = 0.3894 r_free = 0.3894 target = 0.145239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120429 restraints weight = 26637.275| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.14 r_work: 0.3456 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17574 Z= 0.141 Angle : 0.600 8.562 23886 Z= 0.315 Chirality : 0.043 0.163 2604 Planarity : 0.005 0.061 3069 Dihedral : 4.776 25.009 2349 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 12.60 % Favored : 85.03 % 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: -0.02 (0.18), residues: 2133 helix: 1.34 (0.26), residues: 381 sheet: -0.02 (0.21), residues: 558 loop : -0.41 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 574 TYR 0.022 0.002 TYR K 713 PHE 0.016 0.002 PHE C 118 TRP 0.008 0.001 TRP G 180 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17532) covalent geometry : angle 0.59004 / 0.31 (23784) SS BOND : bond 0.00292 / 0.21 ( 24) SS BOND : angle 1.94324 / 1.27 ( 48) hydrogen bonds : bond 0.04424 / 2.85 ( 741) hydrogen bonds : angle 5.78547 / 4.01 ( 1971) link_BETA1-4 : bond 0.00158 / 0.08 ( 3) link_BETA1-4 : angle 1.38680 / 0.84 ( 9) link_NAG-ASN : bond 0.00268 / 0.18 ( 15) link_NAG-ASN : angle 1.70306 / 1.10 ( 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 339 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8645 (m) REVERT: B 389 MET cc_start: 0.9040 (mmm) cc_final: 0.8698 (mmm) REVERT: B 402 LYS cc_start: 0.8299 (mttm) cc_final: 0.8069 (mtmm) REVERT: H 526 LYS cc_start: 0.7472 (tttt) cc_final: 0.6973 (ttpt) REVERT: H 584 SER cc_start: 0.8651 (m) cc_final: 0.8328 (p) REVERT: H 600 VAL cc_start: 0.6974 (t) cc_final: 0.6704 (p) REVERT: L 687 SER cc_start: 0.9197 (p) cc_final: 0.8749 (m) REVERT: L 692 ASP cc_start: 0.5577 (t0) cc_final: 0.5249 (p0) REVERT: L 694 THR cc_start: 0.8416 (m) cc_final: 0.8089 (p) REVERT: L 713 TYR cc_start: 0.8272 (p90) cc_final: 0.8070 (p90) REVERT: C 25 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: D 402 LYS cc_start: 0.8291 (mttm) cc_final: 0.8083 (mtmm) REVERT: E 539 TYR cc_start: 0.8466 (m-80) cc_final: 0.8058 (m-80) REVERT: E 584 SER cc_start: 0.8589 (m) cc_final: 0.8141 (p) REVERT: F 638 GLU cc_start: 0.5989 (pt0) cc_final: 0.5579 (pt0) REVERT: F 687 SER cc_start: 0.8814 (p) cc_final: 0.8383 (m) REVERT: F 692 ASP cc_start: 0.5479 (t0) cc_final: 0.4996 (p0) REVERT: G 25 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: G 173 GLU cc_start: 0.7410 (tp30) cc_final: 0.7137 (tp30) REVERT: G 301 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8684 (m) REVERT: I 469 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7853 (mm-30) REVERT: J 526 LYS cc_start: 0.7483 (tttt) cc_final: 0.6850 (ttpt) REVERT: J 584 SER cc_start: 0.8564 (m) cc_final: 0.8299 (p) REVERT: K 687 SER cc_start: 0.8809 (p) cc_final: 0.8337 (m) REVERT: K 692 ASP cc_start: 0.5546 (t0) cc_final: 0.5090 (p0) outliers start: 44 outliers final: 33 residues processed: 321 average time/residue: 0.1312 time to fit residues: 65.3457 Evaluate side-chains 312 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 578 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 345 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 172 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117718 restraints weight = 26846.617| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.14 r_work: 0.3418 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17574 Z= 0.189 Angle : 0.628 8.455 23886 Z= 0.326 Chirality : 0.044 0.174 2604 Planarity : 0.005 0.074 3069 Dihedral : 4.702 21.997 2349 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.39 % Allowed : 12.17 % Favored : 84.44 % 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: 1.39 (0.25), residues: 381 sheet: -0.00 (0.22), residues: 534 loop : -0.51 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 436 TYR 0.021 0.002 TYR H 610 PHE 0.021 0.002 PHE I 440 TRP 0.012 0.001 TRP G 153 HIS 0.009 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (17532) covalent geometry : angle 0.61636 / 0.32 (23784) SS BOND : bond 0.00428 / 0.30 ( 24) SS BOND : angle 2.20237 / 1.36 ( 48) hydrogen bonds : bond 0.04452 / 2.87 ( 741) hydrogen bonds : angle 5.79442 / 4.01 ( 1971) link_BETA1-4 : bond 0.00052 / 0.03 ( 3) link_BETA1-4 : angle 1.39300 / 0.88 ( 9) link_NAG-ASN : bond 0.00410 / 0.27 ( 15) link_NAG-ASN : angle 1.78114 / 1.15 ( 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 345 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7645 (mtm-85) REVERT: A 301 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8592 (m) REVERT: B 389 MET cc_start: 0.9054 (mmm) cc_final: 0.8627 (mmm) REVERT: B 471 TYR cc_start: 0.6638 (m-80) cc_final: 0.6374 (m-80) REVERT: H 526 LYS cc_start: 0.7489 (tttt) cc_final: 0.7007 (ttpt) REVERT: H 584 SER cc_start: 0.8687 (m) cc_final: 0.8339 (p) REVERT: H 600 VAL cc_start: 0.6921 (OUTLIER) cc_final: 0.6683 (p) REVERT: L 627 GLN cc_start: 0.6986 (tm-30) cc_final: 0.6771 (tm-30) REVERT: L 634 LEU cc_start: 0.8191 (mm) cc_final: 0.7759 (mt) REVERT: L 687 SER cc_start: 0.9246 (p) cc_final: 0.8754 (m) REVERT: L 692 ASP cc_start: 0.5902 (t0) cc_final: 0.5498 (p0) REVERT: C 25 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: D 402 LYS cc_start: 0.8396 (mttm) cc_final: 0.8196 (mtmm) REVERT: E 539 TYR cc_start: 0.8506 (m-80) cc_final: 0.8228 (m-80) REVERT: E 584 SER cc_start: 0.8652 (m) cc_final: 0.8251 (p) REVERT: E 610 TYR cc_start: 0.8507 (m-80) cc_final: 0.8292 (m-80) REVERT: F 687 SER cc_start: 0.8951 (p) cc_final: 0.8510 (m) REVERT: F 692 ASP cc_start: 0.5916 (t0) cc_final: 0.5254 (p0) REVERT: G 25 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: G 173 GLU cc_start: 0.7256 (tp30) cc_final: 0.7026 (tp30) REVERT: I 469 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8080 (mm-30) REVERT: J 526 LYS cc_start: 0.7407 (tttt) cc_final: 0.6767 (ttpt) REVERT: J 584 SER cc_start: 0.8469 (m) cc_final: 0.8242 (p) REVERT: K 687 SER cc_start: 0.8867 (p) cc_final: 0.8409 (m) REVERT: K 692 ASP cc_start: 0.5731 (t0) cc_final: 0.5249 (p0) outliers start: 63 outliers final: 52 residues processed: 315 average time/residue: 0.1305 time to fit residues: 63.8509 Evaluate side-chains 322 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 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 600 VAL Chi-restraints excluded: chain H residue 607 SER Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 696 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 40 SER 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 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 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 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 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 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: 6.9990 chunk 69 optimal weight: 0.0980 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN ** H 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** 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 = 0.3901 r_free = 0.3901 target = 0.145802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121195 restraints weight = 26579.532| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.14 r_work: 0.3469 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17574 Z= 0.110 Angle : 0.566 8.434 23886 Z= 0.292 Chirality : 0.042 0.156 2604 Planarity : 0.005 0.059 3069 Dihedral : 4.501 22.945 2349 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.83 % Allowed : 14.32 % Favored : 83.84 % 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: 0.07 (0.18), residues: 2133 helix: 1.57 (0.26), residues: 381 sheet: 0.05 (0.22), residues: 534 loop : -0.41 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 436 TYR 0.031 0.002 TYR L 713 PHE 0.014 0.001 PHE C 118 TRP 0.008 0.001 TRP A 64 HIS 0.005 0.001 HIS D 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17532) covalent geometry : angle 0.55475 / 0.29 (23784) SS BOND : bond 0.00268 / 0.19 ( 24) SS BOND : angle 2.16976 / 1.37 ( 48) hydrogen bonds : bond 0.04004 / 2.60 ( 741) hydrogen bonds : angle 5.58586 / 3.89 ( 1971) link_BETA1-4 : bond 0.00233 / 0.12 ( 3) link_BETA1-4 : angle 1.21680 / 0.77 ( 9) link_NAG-ASN : bond 0.00210 / 0.14 ( 15) link_NAG-ASN : angle 1.52514 / 0.99 ( 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 305 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8375 (m-80) cc_final: 0.8151 (m-80) REVERT: A 301 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8558 (m) REVERT: B 389 MET cc_start: 0.8996 (mmm) cc_final: 0.8586 (mmm) REVERT: B 419 LEU cc_start: 0.9105 (tt) cc_final: 0.8891 (tt) REVERT: B 471 TYR cc_start: 0.6610 (m-80) cc_final: 0.6376 (m-80) REVERT: H 584 SER cc_start: 0.8668 (m) cc_final: 0.8352 (p) REVERT: H 600 VAL cc_start: 0.6822 (OUTLIER) cc_final: 0.6584 (p) REVERT: L 634 LEU cc_start: 0.8156 (mm) cc_final: 0.7713 (mt) REVERT: L 687 SER cc_start: 0.9174 (p) cc_final: 0.8754 (m) REVERT: L 692 ASP cc_start: 0.5820 (t0) cc_final: 0.5454 (p0) REVERT: C 25 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: E 539 TYR cc_start: 0.8417 (m-80) cc_final: 0.8207 (m-80) REVERT: E 584 SER cc_start: 0.8527 (m) cc_final: 0.8227 (p) REVERT: F 687 SER cc_start: 0.8929 (p) cc_final: 0.8480 (m) REVERT: F 692 ASP cc_start: 0.5738 (t0) cc_final: 0.5173 (p0) REVERT: G 25 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: I 469 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7936 (mm-30) REVERT: J 526 LYS cc_start: 0.7509 (tttt) cc_final: 0.6890 (ttpt) REVERT: K 687 SER cc_start: 0.8856 (p) cc_final: 0.8383 (m) REVERT: K 692 ASP cc_start: 0.5709 (t0) cc_final: 0.5228 (p0) outliers start: 34 outliers final: 24 residues processed: 296 average time/residue: 0.1293 time to fit residues: 59.7624 Evaluate side-chains 291 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain E residue 518 VAL 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 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 552 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 607 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.0000 chunk 141 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 100 optimal weight: 0.0270 overall best weight: 0.7646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN D 392 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.144889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120270 restraints weight = 26650.914| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.14 r_work: 0.3450 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17574 Z= 0.133 Angle : 0.577 9.073 23886 Z= 0.298 Chirality : 0.042 0.155 2604 Planarity : 0.005 0.059 3069 Dihedral : 4.445 20.770 2349 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.32 % Allowed : 14.00 % Favored : 83.68 % 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: 0.07 (0.18), residues: 2133 helix: 1.65 (0.26), residues: 381 sheet: 0.03 (0.22), residues: 540 loop : -0.43 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 725 TYR 0.031 0.002 TYR E 610 PHE 0.015 0.001 PHE I 440 TRP 0.006 0.001 TRP E 554 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (17532) covalent geometry : angle 0.56623 / 0.29 (23784) SS BOND : bond 0.00347 / 0.24 ( 24) SS BOND : angle 2.16107 / 1.34 ( 48) hydrogen bonds : bond 0.04014 / 2.61 ( 741) hydrogen bonds : angle 5.55022 / 3.85 ( 1971) link_BETA1-4 : bond 0.00125 / 0.06 ( 3) link_BETA1-4 : angle 1.20335 / 0.77 ( 9) link_NAG-ASN : bond 0.00276 / 0.18 ( 15) link_NAG-ASN : angle 1.51015 / 0.99 ( 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 313 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8404 (m-80) cc_final: 0.8133 (m-80) REVERT: A 301 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8511 (m) REVERT: B 389 MET cc_start: 0.8951 (mmm) cc_final: 0.8511 (mmm) REVERT: H 584 SER cc_start: 0.8670 (m) cc_final: 0.8354 (p) REVERT: H 600 VAL cc_start: 0.6893 (OUTLIER) cc_final: 0.6664 (p) REVERT: L 634 LEU cc_start: 0.8167 (mm) cc_final: 0.7738 (mt) REVERT: L 687 SER cc_start: 0.9223 (p) cc_final: 0.8815 (m) REVERT: L 692 ASP cc_start: 0.5827 (t0) cc_final: 0.5467 (p0) REVERT: C 25 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: C 286 GLN cc_start: 0.7710 (mt0) cc_final: 0.7297 (mt0) REVERT: E 584 SER cc_start: 0.8521 (m) cc_final: 0.8250 (p) REVERT: F 687 SER cc_start: 0.8707 (p) cc_final: 0.8266 (m) REVERT: F 692 ASP cc_start: 0.5867 (t0) cc_final: 0.5272 (p0) REVERT: I 433 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7765 (mt-10) REVERT: I 469 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8094 (mm-30) REVERT: I 498 LEU cc_start: 0.8264 (pp) cc_final: 0.7709 (mt) REVERT: K 687 SER cc_start: 0.8893 (p) cc_final: 0.8429 (m) REVERT: K 692 ASP cc_start: 0.5722 (t0) cc_final: 0.5229 (p0) outliers start: 43 outliers final: 34 residues processed: 290 average time/residue: 0.1292 time to fit residues: 58.3432 Evaluate side-chains 297 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 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 275 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 40 SER 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 439 ASP 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 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 650 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN B 390 ASN D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119735 restraints weight = 26689.084| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.15 r_work: 0.3443 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4823 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= 0.139 Angle : 0.578 9.942 23886 Z= 0.298 Chirality : 0.042 0.156 2604 Planarity : 0.004 0.047 3069 Dihedral : 4.406 20.601 2349 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.75 % Allowed : 13.57 % Favored : 83.68 % 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: 1.67 (0.26), residues: 381 sheet: 0.04 (0.23), residues: 540 loop : -0.42 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 725 TYR 0.028 0.002 TYR E 610 PHE 0.015 0.002 PHE I 440 TRP 0.008 0.001 TRP I 422 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17532) covalent geometry : angle 0.56732 / 0.29 (23784) SS BOND : bond 0.00403 / 0.28 ( 24) SS BOND : angle 2.10697 / 1.30 ( 48) hydrogen bonds : bond 0.04008 / 2.60 ( 741) hydrogen bonds : angle 5.48776 / 3.82 ( 1971) link_BETA1-4 : bond 0.00130 / 0.07 ( 3) link_BETA1-4 : angle 1.17815 / 0.75 ( 9) link_NAG-ASN : bond 0.00274 / 0.18 ( 15) link_NAG-ASN : angle 1.50536 / 0.99 ( 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 321 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 270 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7205 (tp30) cc_final: 0.6996 (tp30) REVERT: B 389 MET cc_start: 0.8943 (mmm) cc_final: 0.8476 (mmm) REVERT: H 584 SER cc_start: 0.8661 (m) cc_final: 0.8350 (p) REVERT: H 600 VAL cc_start: 0.6933 (OUTLIER) cc_final: 0.6714 (p) REVERT: H 614 PRO cc_start: 0.8417 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8202 (mm) cc_final: 0.7773 (mt) REVERT: L 687 SER cc_start: 0.9181 (p) cc_final: 0.8813 (m) REVERT: L 692 ASP cc_start: 0.5961 (t0) cc_final: 0.5596 (p0) REVERT: C 25 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: C 199 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7447 (p0) REVERT: C 286 GLN cc_start: 0.7740 (mt0) cc_final: 0.7334 (mt0) REVERT: E 584 SER cc_start: 0.8511 (m) cc_final: 0.8267 (p) REVERT: E 614 PRO cc_start: 0.8417 (Cg_endo) cc_final: 0.8184 (Cg_exo) REVERT: F 687 SER cc_start: 0.8691 (p) cc_final: 0.8285 (m) REVERT: F 692 ASP cc_start: 0.5852 (t0) cc_final: 0.5286 (p0) REVERT: G 25 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: G 173 GLU cc_start: 0.7458 (tp30) cc_final: 0.7255 (tp30) REVERT: I 433 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7779 (mt-10) REVERT: I 498 LEU cc_start: 0.8275 (pp) cc_final: 0.7721 (mt) REVERT: K 687 SER cc_start: 0.8895 (p) cc_final: 0.8469 (m) REVERT: K 692 ASP cc_start: 0.5784 (t0) cc_final: 0.5285 (p0) outliers start: 51 outliers final: 43 residues processed: 296 average time/residue: 0.1245 time to fit residues: 58.4370 Evaluate side-chains 305 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 25 GLU Chi-restraints excluded: chain C residue 40 SER 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 352 TYR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 576 THR 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 F residue 642 LEU 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 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 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 K residue 641 THR Chi-restraints excluded: chain K residue 650 VAL 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: 0.5980 chunk 138 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 chunk 175 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120398 restraints weight = 26768.137| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.16 r_work: 0.3453 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17574 Z= 0.127 Angle : 0.567 9.506 23886 Z= 0.292 Chirality : 0.042 0.154 2604 Planarity : 0.004 0.064 3069 Dihedral : 4.363 20.886 2349 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.37 % Allowed : 14.05 % Favored : 83.58 % 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: 0.10 (0.18), residues: 2133 helix: 1.70 (0.26), residues: 381 sheet: 0.08 (0.23), residues: 540 loop : -0.43 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 436 TYR 0.026 0.001 TYR E 610 PHE 0.014 0.001 PHE I 440 TRP 0.005 0.001 TRP G 153 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17532) covalent geometry : angle 0.55653 / 0.29 (23784) SS BOND : bond 0.00350 / 0.25 ( 24) SS BOND : angle 2.08416 / 1.31 ( 48) hydrogen bonds : bond 0.03924 / 2.56 ( 741) hydrogen bonds : angle 5.44156 / 3.78 ( 1971) link_BETA1-4 : bond 0.00135 / 0.07 ( 3) link_BETA1-4 : angle 1.14865 / 0.73 ( 9) link_NAG-ASN : bond 0.00254 / 0.17 ( 15) link_NAG-ASN : angle 1.45908 / 0.96 ( 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 315 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7241 (tp30) cc_final: 0.7012 (tp30) REVERT: B 389 MET cc_start: 0.8931 (mmm) cc_final: 0.8454 (mmm) REVERT: H 584 SER cc_start: 0.8671 (m) cc_final: 0.8361 (p) REVERT: H 600 VAL cc_start: 0.6910 (OUTLIER) cc_final: 0.6698 (p) REVERT: H 614 PRO cc_start: 0.8511 (Cg_endo) cc_final: 0.8213 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8086 (mm) cc_final: 0.7663 (mt) REVERT: L 687 SER cc_start: 0.9101 (p) cc_final: 0.8764 (m) REVERT: L 692 ASP cc_start: 0.5967 (t0) cc_final: 0.5594 (p0) REVERT: C 199 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7459 (p0) REVERT: C 286 GLN cc_start: 0.7758 (mt0) cc_final: 0.7359 (mt0) REVERT: F 687 SER cc_start: 0.8698 (p) cc_final: 0.8322 (m) REVERT: F 692 ASP cc_start: 0.5887 (t0) cc_final: 0.5304 (p0) REVERT: G 173 GLU cc_start: 0.7428 (tp30) cc_final: 0.7221 (tp30) REVERT: I 433 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7769 (mt-10) REVERT: I 469 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8132 (mm-30) REVERT: I 498 LEU cc_start: 0.8261 (pp) cc_final: 0.7703 (mt) REVERT: K 687 SER cc_start: 0.8951 (p) cc_final: 0.8437 (m) REVERT: K 692 ASP cc_start: 0.5904 (t0) cc_final: 0.5417 (p0) outliers start: 44 outliers final: 38 residues processed: 294 average time/residue: 0.1318 time to fit residues: 60.1164 Evaluate side-chains 301 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 C residue 260 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 576 THR 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 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 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 552 LEU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 650 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120076 restraints weight = 26417.075| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.08 r_work: 0.3458 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5016 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= 0.133 Angle : 0.573 10.453 23886 Z= 0.294 Chirality : 0.042 0.154 2604 Planarity : 0.004 0.071 3069 Dihedral : 4.343 20.681 2349 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.32 % Allowed : 14.22 % Favored : 83.47 % 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: 0.11 (0.18), residues: 2133 helix: 1.71 (0.26), residues: 381 sheet: 0.15 (0.23), residues: 543 loop : -0.46 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 725 TYR 0.025 0.001 TYR L 713 PHE 0.014 0.001 PHE I 440 TRP 0.007 0.001 TRP A 255 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17532) covalent geometry : angle 0.56297 / 0.29 (23784) SS BOND : bond 0.00346 / 0.24 ( 24) SS BOND : angle 2.00662 / 1.27 ( 48) hydrogen bonds : bond 0.03913 / 2.54 ( 741) hydrogen bonds : angle 5.42776 / 3.77 ( 1971) link_BETA1-4 : bond 0.00133 / 0.07 ( 3) link_BETA1-4 : angle 1.15715 / 0.74 ( 9) link_NAG-ASN : bond 0.00267 / 0.18 ( 15) link_NAG-ASN : angle 1.46139 / 0.97 ( 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 314 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7238 (tp30) cc_final: 0.7021 (tp30) REVERT: B 389 MET cc_start: 0.8915 (mmm) cc_final: 0.8431 (mmm) REVERT: H 584 SER cc_start: 0.8677 (m) cc_final: 0.8367 (p) REVERT: H 600 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6697 (p) REVERT: H 614 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8190 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8099 (mm) cc_final: 0.7674 (mt) REVERT: L 687 SER cc_start: 0.9015 (p) cc_final: 0.8688 (m) REVERT: L 692 ASP cc_start: 0.5981 (t0) cc_final: 0.5615 (p0) REVERT: C 25 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: C 199 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7499 (p0) REVERT: C 279 ASP cc_start: 0.6399 (t0) cc_final: 0.5983 (p0) REVERT: C 286 GLN cc_start: 0.7779 (mt0) cc_final: 0.7382 (mt0) REVERT: D 498 LEU cc_start: 0.8553 (pp) cc_final: 0.8043 (mt) REVERT: F 687 SER cc_start: 0.8723 (p) cc_final: 0.8367 (m) REVERT: G 120 ILE cc_start: 0.8141 (tt) cc_final: 0.7805 (tt) REVERT: G 173 GLU cc_start: 0.7394 (tp30) cc_final: 0.7186 (tp30) REVERT: I 469 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8092 (mm-30) REVERT: I 498 LEU cc_start: 0.8264 (pp) cc_final: 0.7717 (mt) REVERT: J 545 ARG cc_start: 0.6990 (ttp-170) cc_final: 0.6728 (ttm170) REVERT: J 597 ASP cc_start: 0.7472 (m-30) cc_final: 0.7148 (m-30) REVERT: K 632 LEU cc_start: 0.6814 (tp) cc_final: 0.6480 (mp) REVERT: K 687 SER cc_start: 0.8854 (p) cc_final: 0.8307 (m) REVERT: K 692 ASP cc_start: 0.5896 (t0) cc_final: 0.5521 (p0) outliers start: 43 outliers final: 40 residues processed: 293 average time/residue: 0.1316 time to fit residues: 60.1549 Evaluate side-chains 303 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 199 ASN 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 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 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 260 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 576 THR 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 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 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 K residue 641 THR Chi-restraints excluded: chain K residue 650 VAL 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: 8.9990 chunk 136 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 123 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118601 restraints weight = 26834.132| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.14 r_work: 0.3432 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5102 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= 0.162 Angle : 0.594 9.879 23886 Z= 0.305 Chirality : 0.043 0.156 2604 Planarity : 0.005 0.070 3069 Dihedral : 4.412 20.600 2349 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.75 % Allowed : 14.32 % 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: 0.06 (0.18), residues: 2133 helix: 1.64 (0.26), residues: 381 sheet: 0.12 (0.23), residues: 543 loop : -0.48 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 683 TYR 0.026 0.002 TYR E 610 PHE 0.016 0.002 PHE I 440 TRP 0.009 0.001 TRP A 255 HIS 0.006 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (17532) covalent geometry : angle 0.58385 / 0.30 (23784) SS BOND : bond 0.00394 / 0.27 ( 24) SS BOND : angle 1.99945 / 1.27 ( 48) hydrogen bonds : bond 0.04013 / 2.61 ( 741) hydrogen bonds : angle 5.48161 / 3.80 ( 1971) link_BETA1-4 : bond 0.00085 / 0.04 ( 3) link_BETA1-4 : angle 1.19274 / 0.75 ( 9) link_NAG-ASN : bond 0.00323 / 0.22 ( 15) link_NAG-ASN : angle 1.53547 / 1.02 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.05 seconds wall clock time: 81 minutes 4.61 seconds (4864.61 seconds total)