Starting phenix.real_space_refine on Sun Aug 24 05:43:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2m_44112/08_2025/9b2m_44112.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2m_44112/08_2025/9b2m_44112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2m_44112/08_2025/9b2m_44112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2m_44112/08_2025/9b2m_44112.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2m_44112/08_2025/9b2m_44112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2m_44112/08_2025/9b2m_44112.cif" } resolution = 3.09 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= 0.001 sd= 0.038 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 75 5.16 5 C 11007 2.51 5 N 2955 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 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17412 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "G" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "I" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "J" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.39, per 1000 atoms: 0.25 Number of scatterers: 17412 At special positions: 0 Unit cell: (138.985, 136.895, 143.165, 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 75 16.00 O 3375 8.00 N 2955 7.00 C 11007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.05 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.05 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 478 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.05 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.17 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 278 " distance=2.04 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 71 " distance=2.05 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 139 " distance=2.05 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 306 " distance=2.02 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 478 " distance=2.17 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.06 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=1, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 27 " " NAG A 402 " - " ASN A 91 " " NAG A 403 " - " ASN A 129 " " NAG A 404 " - " ASN A 290 " " NAG A 405 " - " ASN A 58 " " NAG C 401 " - " ASN C 27 " " NAG C 402 " - " ASN C 91 " " NAG C 403 " - " ASN C 129 " " NAG C 405 " - " ASN C 58 " " NAG G 401 " - " ASN G 27 " " NAG G 402 " - " ASN G 91 " " NAG G 403 " - " ASN G 129 " " NAG G 404 " - " ASN G 290 " " NAG G 405 " - " ASN G 58 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 896.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 18.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 77 removed outlier: 5.485A pdb=" N LEU C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 removed outlier: 3.988A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'D' and resid 373 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 492 Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 77 removed outlier: 5.485A pdb=" N LEU A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.988A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'B' and resid 373 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 492 Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 68 through 77 removed outlier: 5.485A pdb=" N LEU G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 111 removed outlier: 3.988A pdb=" N SER G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'I' and resid 373 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 492 Processing helix chain 'I' and resid 497 through 502 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'D' and resid 361 through 366 removed outlier: 3.911A pdb=" N GLU D 462 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 48 removed outlier: 7.809A pdb=" N LEU C 45 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ALA C 280 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU C 47 " --> pdb=" O ALA C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.223A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 118 removed outlier: 6.999A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU C 251 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 118 removed outlier: 6.999A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'C' and resid 287 through 289 removed outlier: 4.026A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 67 through 72 removed outlier: 4.364A pdb=" N GLN H 116 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN H 6 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.985A pdb=" N VAL H 11 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.985A pdb=" N VAL H 11 " --> pdb=" O THR H 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 12 through 13 removed outlier: 5.357A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 361 through 366 removed outlier: 3.912A pdb=" N GLU B 462 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AC1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AC2, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.810A pdb=" N LEU A 45 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA A 280 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A 47 " --> pdb=" O ALA A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.223A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 112 through 118 removed outlier: 6.998A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A 251 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 112 through 118 removed outlier: 6.998A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.027A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 67 through 72 removed outlier: 4.364A pdb=" N GLN E 116 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN E 6 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.985A pdb=" N VAL E 11 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.985A pdb=" N VAL E 11 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'F' and resid 12 through 13 removed outlier: 5.356A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 361 through 366 removed outlier: 3.912A pdb=" N GLU I 462 " --> pdb=" O GLU I 469 " (cutoff:3.500A) 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 45 through 48 removed outlier: 7.810A pdb=" N LEU G 45 " --> pdb=" O CYS G 278 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA G 280 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU G 47 " --> pdb=" O ALA G 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'G' and resid 54 through 57 removed outlier: 6.223A pdb=" N ILE G 83 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 112 through 118 removed outlier: 6.999A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU G 251 " --> pdb=" O LEU G 154 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 112 through 118 removed outlier: 6.999A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (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 removed outlier: 4.028A pdb=" N CYS G 282 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 67 through 72 removed outlier: 4.363A pdb=" N GLN J 116 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN J 6 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.985A pdb=" N VAL J 11 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.985A pdb=" N VAL J 11 " --> pdb=" O THR J 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'K' and resid 12 through 13 removed outlier: 5.357A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4313 1.32 - 1.46: 5825 1.46 - 1.60: 7565 1.60 - 1.74: 27 1.74 - 1.88: 96 Bond restraints: 17826 Sorted by residual: bond pdb=" C GLY B 350 " pdb=" O GLY B 350 " ideal model delta sigma weight residual 1.230 1.351 -0.121 1.37e-02 5.33e+03 7.77e+01 bond pdb=" CB PHE C 245 " pdb=" CG PHE C 245 " ideal model delta sigma weight residual 1.502 1.313 0.189 2.30e-02 1.89e+03 6.75e+01 bond pdb=" CB PHE G 245 " pdb=" CG PHE G 245 " ideal model delta sigma weight residual 1.502 1.313 0.189 2.30e-02 1.89e+03 6.73e+01 bond pdb=" CB PHE A 245 " pdb=" CG PHE A 245 " ideal model delta sigma weight residual 1.502 1.314 0.188 2.30e-02 1.89e+03 6.70e+01 bond pdb=" CB HIS C 41 " pdb=" CG HIS C 41 " ideal model delta sigma weight residual 1.497 1.392 0.105 1.40e-02 5.10e+03 5.67e+01 ... (remaining 17821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 23430 4.66 - 9.32: 725 9.32 - 13.99: 22 13.99 - 18.65: 1 18.65 - 23.31: 2 Bond angle restraints: 24180 Sorted by residual: angle pdb=" N TRP I 351 " pdb=" CA TRP I 351 " pdb=" C TRP I 351 " ideal model delta sigma weight residual 113.18 89.87 23.31 1.33e+00 5.65e-01 3.07e+02 angle pdb=" N TRP D 351 " pdb=" CA TRP D 351 " pdb=" C TRP D 351 " ideal model delta sigma weight residual 111.36 97.18 14.18 1.09e+00 8.42e-01 1.69e+02 angle pdb=" O GLY I 350 " pdb=" C GLY I 350 " pdb=" N TRP I 351 " ideal model delta sigma weight residual 123.27 114.38 8.89 7.60e-01 1.73e+00 1.37e+02 angle pdb=" N TRP B 351 " pdb=" CA TRP B 351 " pdb=" C TRP B 351 " ideal model delta sigma weight residual 110.80 91.16 19.64 2.13e+00 2.20e-01 8.51e+01 angle pdb=" N THR G 319 " pdb=" CA THR G 319 " pdb=" C THR G 319 " ideal model delta sigma weight residual 114.04 103.38 10.66 1.24e+00 6.50e-01 7.39e+01 ... (remaining 24175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 10335 17.13 - 34.25: 332 34.25 - 51.37: 81 51.37 - 68.50: 34 68.50 - 85.62: 12 Dihedral angle restraints: 10794 sinusoidal: 4506 harmonic: 6288 Sorted by residual: dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 478 " pdb=" CB CYS B 478 " ideal model delta sinusoidal sigma weight residual 93.00 25.26 67.74 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS I 474 " pdb=" SG CYS I 474 " pdb=" SG CYS I 478 " pdb=" CB CYS I 478 " ideal model delta sinusoidal sigma weight residual 93.00 25.27 67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS D 474 " pdb=" SG CYS D 474 " pdb=" SG CYS D 478 " pdb=" CB CYS D 478 " ideal model delta sinusoidal sigma weight residual 93.00 25.28 67.72 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 10791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1816 0.107 - 0.213: 696 0.213 - 0.320: 90 0.320 - 0.427: 29 0.427 - 0.533: 23 Chirality restraints: 2654 Sorted by residual: chirality pdb=" CB ILE I 503 " pdb=" CA ILE I 503 " pdb=" CG1 ILE I 503 " pdb=" CG2 ILE I 503 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CB ILE B 503 " pdb=" CA ILE B 503 " pdb=" CG1 ILE B 503 " pdb=" CG2 ILE B 503 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" CB ILE D 503 " pdb=" CA ILE D 503 " pdb=" CG1 ILE D 503 " pdb=" CG2 ILE D 503 " both_signs ideal model delta sigma weight residual False 2.64 3.17 -0.53 2.00e-01 2.50e+01 7.01e+00 ... (remaining 2651 not shown) Planarity restraints: 3119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 290 " 0.078 2.00e-02 2.50e+03 7.97e-02 7.93e+01 pdb=" CG ASN G 290 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN G 290 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN G 290 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG G 404 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 290 " -0.078 2.00e-02 2.50e+03 7.95e-02 7.91e+01 pdb=" CG ASN A 290 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 290 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 290 " 0.121 2.00e-02 2.50e+03 pdb=" C1 NAG A 404 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 350 " -0.042 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" C GLY B 350 " 0.147 2.00e-02 2.50e+03 pdb=" O GLY B 350 " -0.052 2.00e-02 2.50e+03 pdb=" N TRP B 351 " -0.053 2.00e-02 2.50e+03 ... (remaining 3116 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 14 2.18 - 2.86: 6033 2.86 - 3.54: 23725 3.54 - 4.22: 45122 4.22 - 4.90: 72770 Nonbonded interactions: 147664 Sorted by model distance: nonbonded pdb=" CZ2 TRP H 50 " pdb=" OE2 GLU H 95 " model vdw 1.499 3.340 nonbonded pdb=" CZ2 TRP E 50 " pdb=" OE2 GLU E 95 " model vdw 1.499 3.340 nonbonded pdb=" CZ2 TRP J 50 " pdb=" OE2 GLU J 95 " model vdw 1.500 3.340 nonbonded pdb=" CE LYS C 281 " pdb=" OE2 GLU C 305 " model vdw 1.604 3.440 nonbonded pdb=" CH2 TRP H 50 " pdb=" OE2 GLU H 95 " model vdw 1.663 3.340 ... (remaining 147659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.240 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 0.023 0.226 17862 Z= 1.221 Angle : 1.915 23.309 24264 Z= 1.282 Chirality : 0.116 0.533 2654 Planarity : 0.009 0.085 3105 Dihedral : 9.981 85.623 6717 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.26 % Allowed : 0.84 % Favored : 98.89 % Cbeta Deviations : 0.15 % 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 aren not related in a simple way. whole: 0.77 (0.17), residues: 2163 helix: -0.04 (0.23), residues: 330 sheet: 1.54 (0.24), residues: 453 loop : 0.39 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 229 TYR 0.058 0.010 TYR B 471 PHE 0.063 0.009 PHE G 115 TRP 0.038 0.009 TRP J 47 HIS 0.012 0.003 HIS D 472 Details of bonding type rmsd covalent geometry : bond 0.02254 (17826) covalent geometry : angle 1.90737 (24180) SS BOND : bond 0.05638 ( 21) SS BOND : angle 3.78007 ( 42) hydrogen bonds : bond 0.16089 ( 657) hydrogen bonds : angle 7.67178 ( 1731) Misc. bond : bond 0.22558 ( 1) link_NAG-ASN : bond 0.08353 ( 14) link_NAG-ASN : angle 2.98003 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 507 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 396 VAL cc_start: 0.7729 (t) cc_final: 0.7459 (p) REVERT: L 79 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5031 (tm-30) REVERT: A 290 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7983 (p0) REVERT: B 351 TRP cc_start: 0.7237 (OUTLIER) cc_final: 0.6302 (t60) REVERT: F 79 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5683 (mm-30) REVERT: I 484 ASN cc_start: 0.4921 (m-40) cc_final: 0.4713 (m-40) REVERT: K 35 TRP cc_start: 0.6681 (m100) cc_final: 0.6004 (m100) REVERT: K 79 GLU cc_start: 0.6182 (mt-10) cc_final: 0.5684 (mp0) outliers start: 5 outliers final: 2 residues processed: 511 average time/residue: 0.1235 time to fit residues: 95.2139 Evaluate side-chains 296 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 351 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 HIS C 190 ASN C 290 ASN D 355 HIS D 401 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 53 ASN A 32 HIS A 141 HIS A 190 ASN B 355 HIS B 368 GLN B 401 ASN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 53 ASN G 141 HIS G 190 ASN I 401 ASN I 409 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 30 ASN K 38 GLN K 53 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.191417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150199 restraints weight = 25270.540| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.59 r_work: 0.3812 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17862 Z= 0.184 Angle : 0.730 10.607 24264 Z= 0.378 Chirality : 0.047 0.207 2654 Planarity : 0.005 0.044 3105 Dihedral : 6.140 45.584 2675 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.90 % Allowed : 8.32 % Favored : 88.78 % 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 aren not related in a simple way. whole: 0.35 (0.18), residues: 2163 helix: 0.72 (0.26), residues: 360 sheet: 1.06 (0.24), residues: 468 loop : -0.16 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.020 0.002 TYR H 79 PHE 0.032 0.003 PHE H 103 TRP 0.027 0.002 TRP J 105 HIS 0.009 0.002 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00406 (17826) covalent geometry : angle 0.72213 (24180) SS BOND : bond 0.00860 ( 21) SS BOND : angle 1.47848 ( 42) hydrogen bonds : bond 0.05507 ( 657) hydrogen bonds : angle 6.00936 ( 1731) Misc. bond : bond 0.00110 ( 1) link_NAG-ASN : bond 0.00499 ( 14) link_NAG-ASN : angle 2.32016 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 384 time to evaluate : 0.647 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: C 219 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7643 (ptmt) REVERT: C 229 ARG cc_start: 0.7424 (ptt-90) cc_final: 0.6328 (mtt90) REVERT: C 264 PHE cc_start: 0.6672 (p90) cc_final: 0.6254 (t80) REVERT: C 276 ASP cc_start: 0.6525 (p0) cc_final: 0.6152 (p0) REVERT: D 396 VAL cc_start: 0.7864 (t) cc_final: 0.7584 (p) REVERT: D 407 MET cc_start: 0.8040 (ttm) cc_final: 0.7522 (ttm) REVERT: D 446 LYS cc_start: 0.8128 (tppt) cc_final: 0.7811 (mttt) REVERT: D 474 CYS cc_start: 0.3249 (m) cc_final: 0.2922 (m) REVERT: L 79 GLU cc_start: 0.5865 (mt-10) cc_final: 0.5610 (mp0) REVERT: A 264 PHE cc_start: 0.6965 (p90) cc_final: 0.6343 (t80) REVERT: B 347 MET cc_start: 0.6371 (ttp) cc_final: 0.6104 (ttp) REVERT: B 407 MET cc_start: 0.7611 (tpp) cc_final: 0.7306 (ttm) REVERT: B 435 GLU cc_start: 0.8017 (tp30) cc_final: 0.7809 (tp30) REVERT: E 48 MET cc_start: 0.8443 (mmm) cc_final: 0.8163 (mmt) REVERT: E 106 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7475 (mp) REVERT: G 51 ILE cc_start: 0.8064 (mp) cc_final: 0.7761 (tp) REVERT: G 229 ARG cc_start: 0.7326 (ptt-90) cc_final: 0.6290 (mtt90) REVERT: G 245 PHE cc_start: 0.7596 (t80) cc_final: 0.7154 (t80) REVERT: G 264 PHE cc_start: 0.6745 (p90) cc_final: 0.6325 (t80) REVERT: I 488 ASP cc_start: 0.7732 (p0) cc_final: 0.7464 (p0) REVERT: K 35 TRP cc_start: 0.6380 (m100) cc_final: 0.6004 (m100) outliers start: 55 outliers final: 27 residues processed: 417 average time/residue: 0.1332 time to fit residues: 83.4158 Evaluate side-chains 325 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 356 HIS Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 375 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS C 32 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN D 401 ASN D 455 GLN D 472 HIS D 476 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN B 455 GLN B 472 HIS E 6 GLN E 58 ASN F 30 ASN G 12 HIS G 32 HIS ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 ASN ** I 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 484 ASN J 6 GLN J 58 ASN K 30 ASN K 38 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140785 restraints weight = 25385.211| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.36 r_work: 0.3730 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17862 Z= 0.197 Angle : 0.707 15.449 24264 Z= 0.365 Chirality : 0.048 0.488 2654 Planarity : 0.005 0.048 3105 Dihedral : 5.853 56.197 2669 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.90 % Allowed : 10.85 % Favored : 86.26 % 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 aren not related in a simple way. whole: -0.00 (0.18), residues: 2163 helix: 0.46 (0.26), residues: 375 sheet: 0.78 (0.24), residues: 468 loop : -0.40 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 436 TYR 0.015 0.002 TYR A 209 PHE 0.022 0.002 PHE H 103 TRP 0.028 0.002 TRP E 36 HIS 0.010 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00449 (17826) covalent geometry : angle 0.68960 (24180) SS BOND : bond 0.00656 ( 21) SS BOND : angle 1.69137 ( 42) hydrogen bonds : bond 0.05119 ( 657) hydrogen bonds : angle 5.78821 ( 1731) Misc. bond : bond 0.00070 ( 1) link_NAG-ASN : bond 0.00682 ( 14) link_NAG-ASN : angle 3.53795 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.4063 (p90) REVERT: C 229 ARG cc_start: 0.7435 (ptt-90) cc_final: 0.6312 (mtt90) REVERT: C 264 PHE cc_start: 0.6850 (p90) cc_final: 0.6493 (t80) REVERT: D 407 MET cc_start: 0.8052 (ttm) cc_final: 0.7718 (ttm) REVERT: D 446 LYS cc_start: 0.8143 (tppt) cc_final: 0.7840 (mttt) REVERT: L 30 ASN cc_start: 0.5777 (t0) cc_final: 0.5565 (t0) REVERT: L 79 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5881 (mp0) REVERT: A 209 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5565 (p90) REVERT: A 264 PHE cc_start: 0.7046 (p90) cc_final: 0.6661 (t80) REVERT: B 407 MET cc_start: 0.8006 (tpp) cc_final: 0.7762 (ttm) REVERT: B 435 GLU cc_start: 0.8318 (tp30) cc_final: 0.7996 (tp30) REVERT: B 446 LYS cc_start: 0.8100 (tppt) cc_final: 0.7708 (mttt) REVERT: E 46 GLU cc_start: 0.4949 (pm20) cc_final: 0.4614 (pm20) REVERT: E 106 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7414 (mp) REVERT: G 209 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.5044 (p90) REVERT: G 229 ARG cc_start: 0.7373 (ptt-90) cc_final: 0.6297 (mtt90) REVERT: I 446 LYS cc_start: 0.8137 (tppt) cc_final: 0.7899 (mttt) REVERT: I 488 ASP cc_start: 0.7547 (p0) cc_final: 0.7289 (p0) REVERT: K 30 ASN cc_start: 0.6187 (m-40) cc_final: 0.5873 (m110) REVERT: K 79 GLU cc_start: 0.6248 (mp0) cc_final: 0.5581 (mp0) outliers start: 55 outliers final: 29 residues processed: 376 average time/residue: 0.1292 time to fit residues: 73.2006 Evaluate side-chains 317 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 356 HIS Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 375 ILE Chi-restraints excluded: chain K residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 160 optimal weight: 0.0770 chunk 138 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN D 409 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 476 ASN F 30 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 196 HIS I 455 GLN I 472 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.188212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141918 restraints weight = 25381.536| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.32 r_work: 0.3763 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17862 Z= 0.149 Angle : 0.656 14.542 24264 Z= 0.332 Chirality : 0.046 0.561 2654 Planarity : 0.004 0.047 3105 Dihedral : 5.292 50.368 2669 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.05 % Allowed : 12.32 % Favored : 84.62 % 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 aren not related in a simple way. whole: -0.02 (0.18), residues: 2163 helix: 0.54 (0.27), residues: 360 sheet: 0.82 (0.25), residues: 438 loop : -0.43 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 436 TYR 0.016 0.002 TYR A 11 PHE 0.017 0.002 PHE G 115 TRP 0.026 0.002 TRP A 255 HIS 0.005 0.001 HIS K 34 Details of bonding type rmsd covalent geometry : bond 0.00338 (17826) covalent geometry : angle 0.63781 (24180) SS BOND : bond 0.00342 ( 21) SS BOND : angle 1.97902 ( 42) hydrogen bonds : bond 0.04739 ( 657) hydrogen bonds : angle 5.55495 ( 1731) Misc. bond : bond 0.00064 ( 1) link_NAG-ASN : bond 0.00625 ( 14) link_NAG-ASN : angle 3.26152 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 315 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.4741 (p90) REVERT: C 229 ARG cc_start: 0.7339 (ptt-90) cc_final: 0.6278 (mtt90) REVERT: C 264 PHE cc_start: 0.6870 (p90) cc_final: 0.6525 (t80) REVERT: D 407 MET cc_start: 0.7968 (ttm) cc_final: 0.7449 (ttm) REVERT: D 446 LYS cc_start: 0.8129 (tppt) cc_final: 0.7888 (mttt) REVERT: L 21 ILE cc_start: 0.7181 (tp) cc_final: 0.6938 (mt) REVERT: L 71 PHE cc_start: 0.7505 (m-80) cc_final: 0.7238 (m-80) REVERT: A 209 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5496 (p90) REVERT: A 264 PHE cc_start: 0.7047 (p90) cc_final: 0.6738 (t80) REVERT: A 277 GLU cc_start: 0.8073 (tp30) cc_final: 0.7831 (tp30) REVERT: B 407 MET cc_start: 0.7832 (tpp) cc_final: 0.7612 (ttm) REVERT: B 435 GLU cc_start: 0.8239 (tp30) cc_final: 0.7894 (tp30) REVERT: B 446 LYS cc_start: 0.8116 (tppt) cc_final: 0.7805 (mttt) REVERT: E 36 TRP cc_start: 0.8346 (m100) cc_final: 0.7929 (m100) REVERT: E 46 GLU cc_start: 0.4770 (pm20) cc_final: 0.4562 (pm20) REVERT: E 106 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7287 (mp) REVERT: G 209 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5385 (p90) REVERT: G 229 ARG cc_start: 0.7279 (ptt-90) cc_final: 0.6318 (mtt90) REVERT: G 238 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6903 (mm-30) REVERT: I 435 GLU cc_start: 0.8104 (tp30) cc_final: 0.7856 (tp30) REVERT: K 27 HIS cc_start: 0.5366 (t-170) cc_final: 0.5023 (t-170) REVERT: K 50 LYS cc_start: 0.7441 (mmtp) cc_final: 0.7196 (mmtp) REVERT: K 79 GLU cc_start: 0.6120 (mp0) cc_final: 0.5854 (mp0) outliers start: 58 outliers final: 38 residues processed: 353 average time/residue: 0.1035 time to fit residues: 56.4674 Evaluate side-chains 324 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 375 ILE Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 201 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN ** K 34 HIS ** 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 = 0.4339 r_free = 0.4339 target = 0.183127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136232 restraints weight = 25049.795| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.61 r_work: 0.3656 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17862 Z= 0.231 Angle : 0.737 12.288 24264 Z= 0.376 Chirality : 0.048 0.523 2654 Planarity : 0.005 0.049 3105 Dihedral : 5.663 54.806 2669 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.16 % Allowed : 12.59 % Favored : 84.25 % 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 aren not related in a simple way. whole: -0.36 (0.18), residues: 2163 helix: 0.34 (0.26), residues: 378 sheet: 0.43 (0.25), residues: 450 loop : -0.63 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 436 TYR 0.018 0.002 TYR A 209 PHE 0.023 0.003 PHE G 147 TRP 0.022 0.002 TRP B 351 HIS 0.011 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00533 (17826) covalent geometry : angle 0.71804 (24180) SS BOND : bond 0.00673 ( 21) SS BOND : angle 2.71258 ( 42) hydrogen bonds : bond 0.05050 ( 657) hydrogen bonds : angle 5.80227 ( 1731) Misc. bond : bond 0.00050 ( 1) link_NAG-ASN : bond 0.00560 ( 14) link_NAG-ASN : angle 3.08456 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.4793 (p90) REVERT: C 229 ARG cc_start: 0.7435 (ptt-90) cc_final: 0.6300 (mtt90) REVERT: C 264 PHE cc_start: 0.7008 (p90) cc_final: 0.6665 (t80) REVERT: D 407 MET cc_start: 0.8159 (ttm) cc_final: 0.7712 (ttm) REVERT: A 11 TYR cc_start: 0.8253 (p90) cc_final: 0.8048 (p90) REVERT: A 264 PHE cc_start: 0.7108 (p90) cc_final: 0.6779 (t80) REVERT: B 435 GLU cc_start: 0.8420 (tp30) cc_final: 0.8043 (tp30) REVERT: B 446 LYS cc_start: 0.8171 (tppt) cc_final: 0.7821 (mttt) REVERT: E 36 TRP cc_start: 0.8421 (m100) cc_final: 0.7851 (m100) REVERT: E 46 GLU cc_start: 0.4988 (pm20) cc_final: 0.4683 (pm20) REVERT: E 106 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7463 (mp) REVERT: E 109 ASP cc_start: 0.7122 (t70) cc_final: 0.6898 (p0) REVERT: F 47 LEU cc_start: 0.7744 (pt) cc_final: 0.7431 (pp) REVERT: F 79 GLU cc_start: 0.5922 (mm-30) cc_final: 0.5682 (mm-30) REVERT: G 39 ASP cc_start: 0.8158 (p0) cc_final: 0.7873 (p0) REVERT: G 209 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.4837 (p90) REVERT: G 220 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7650 (mtm110) REVERT: G 229 ARG cc_start: 0.7407 (ptt-90) cc_final: 0.6330 (mtt90) REVERT: I 435 GLU cc_start: 0.8319 (tp30) cc_final: 0.7935 (tp30) REVERT: J 36 TRP cc_start: 0.8379 (m100) cc_final: 0.8154 (m100) REVERT: K 27 HIS cc_start: 0.5452 (t-170) cc_final: 0.5199 (t-170) REVERT: K 79 GLU cc_start: 0.5593 (mp0) cc_final: 0.5390 (mp0) outliers start: 60 outliers final: 46 residues processed: 347 average time/residue: 0.1301 time to fit residues: 67.7610 Evaluate side-chains 330 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 356 HIS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 245 PHE Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 206 optimal weight: 0.4980 chunk 201 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 172 optimal weight: 0.0060 chunk 150 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 88 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS F 38 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 GLN K 30 ASN ** K 34 HIS ** 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 = 0.4393 r_free = 0.4393 target = 0.188308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.146773 restraints weight = 25113.800| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.53 r_work: 0.3753 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17862 Z= 0.130 Angle : 0.640 11.246 24264 Z= 0.324 Chirality : 0.045 0.461 2654 Planarity : 0.004 0.048 3105 Dihedral : 5.147 57.851 2669 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 2.42 % Allowed : 14.17 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.18), residues: 2163 helix: 0.65 (0.26), residues: 378 sheet: 0.50 (0.25), residues: 420 loop : -0.51 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 436 TYR 0.036 0.002 TYR C 11 PHE 0.020 0.002 PHE C 115 TRP 0.032 0.002 TRP K 35 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00291 (17826) covalent geometry : angle 0.62425 (24180) SS BOND : bond 0.00424 ( 21) SS BOND : angle 2.32161 ( 42) hydrogen bonds : bond 0.04546 ( 657) hydrogen bonds : angle 5.45675 ( 1731) Misc. bond : bond 0.00049 ( 1) link_NAG-ASN : bond 0.00495 ( 14) link_NAG-ASN : angle 2.59516 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6734 (p-80) REVERT: C 209 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.2887 (p90) REVERT: C 229 ARG cc_start: 0.7381 (ptt-90) cc_final: 0.6260 (mtt90) REVERT: C 264 PHE cc_start: 0.6886 (p90) cc_final: 0.6589 (t80) REVERT: D 407 MET cc_start: 0.7833 (ttm) cc_final: 0.7376 (ttm) REVERT: D 435 GLU cc_start: 0.8230 (tp30) cc_final: 0.7977 (tp30) REVERT: D 446 LYS cc_start: 0.8168 (tppt) cc_final: 0.7787 (mttt) REVERT: H 30 ARG cc_start: 0.6444 (ptm-80) cc_final: 0.5988 (mpp-170) REVERT: L 35 TRP cc_start: 0.6910 (m100) cc_final: 0.6579 (m100) REVERT: A 209 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.5743 (p90) REVERT: A 264 PHE cc_start: 0.7092 (p90) cc_final: 0.6806 (t80) REVERT: B 388 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7459 (mttt) REVERT: B 435 GLU cc_start: 0.8223 (tp30) cc_final: 0.7891 (tp30) REVERT: B 446 LYS cc_start: 0.8112 (tppt) cc_final: 0.7854 (mttt) REVERT: E 32 PHE cc_start: 0.7493 (m-10) cc_final: 0.7212 (m-10) REVERT: E 36 TRP cc_start: 0.8344 (m100) cc_final: 0.8032 (m100) REVERT: E 106 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7356 (mp) REVERT: F 47 LEU cc_start: 0.7903 (pt) cc_final: 0.7607 (pp) REVERT: G 155 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.8010 (t) REVERT: G 160 LEU cc_start: 0.7499 (pp) cc_final: 0.6991 (mt) REVERT: G 209 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.5503 (p90) REVERT: G 220 ARG cc_start: 0.7795 (mtp-110) cc_final: 0.7524 (mtm110) REVERT: G 229 ARG cc_start: 0.7230 (ptt-90) cc_final: 0.6217 (mtt90) REVERT: G 238 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6956 (mm-30) REVERT: I 435 GLU cc_start: 0.8260 (tp30) cc_final: 0.7962 (tp30) REVERT: I 446 LYS cc_start: 0.8295 (mttt) cc_final: 0.7976 (tppt) REVERT: I 494 GLU cc_start: 0.7824 (pm20) cc_final: 0.7378 (pm20) REVERT: K 27 HIS cc_start: 0.5332 (t-170) cc_final: 0.5080 (t-170) REVERT: K 79 GLU cc_start: 0.5727 (mp0) cc_final: 0.5498 (mp0) outliers start: 46 outliers final: 30 residues processed: 350 average time/residue: 0.1137 time to fit residues: 61.0619 Evaluate side-chains 325 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 245 PHE Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 96 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 283 GLN F 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.187903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146237 restraints weight = 25000.718| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.60 r_work: 0.3746 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17862 Z= 0.140 Angle : 0.648 10.395 24264 Z= 0.327 Chirality : 0.045 0.432 2654 Planarity : 0.004 0.047 3105 Dihedral : 5.075 59.538 2669 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 2.95 % Allowed : 14.17 % Favored : 82.89 % 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 aren not related in a simple way. whole: 0.05 (0.18), residues: 2163 helix: 1.19 (0.27), residues: 354 sheet: 0.54 (0.26), residues: 420 loop : -0.42 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 436 TYR 0.017 0.002 TYR C 11 PHE 0.040 0.002 PHE C 147 TRP 0.034 0.002 TRP K 35 HIS 0.005 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00321 (17826) covalent geometry : angle 0.63444 (24180) SS BOND : bond 0.00377 ( 21) SS BOND : angle 2.22312 ( 42) hydrogen bonds : bond 0.04470 ( 657) hydrogen bonds : angle 5.40245 ( 1731) Misc. bond : bond 0.00070 ( 1) link_NAG-ASN : bond 0.00464 ( 14) link_NAG-ASN : angle 2.43488 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 320 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.3020 (p90) REVERT: C 229 ARG cc_start: 0.7321 (ptt-90) cc_final: 0.6143 (mtt90) REVERT: C 264 PHE cc_start: 0.6838 (p90) cc_final: 0.6607 (t80) REVERT: D 407 MET cc_start: 0.7907 (ttm) cc_final: 0.7426 (ttm) REVERT: D 446 LYS cc_start: 0.8253 (tppt) cc_final: 0.7835 (mttt) REVERT: D 456 LEU cc_start: 0.7484 (mt) cc_final: 0.6873 (tp) REVERT: H 30 ARG cc_start: 0.6655 (ptm-80) cc_final: 0.5649 (mtp180) REVERT: H 32 PHE cc_start: 0.7578 (m-10) cc_final: 0.7194 (m-10) REVERT: H 61 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: L 21 ILE cc_start: 0.8251 (mt) cc_final: 0.8046 (mm) REVERT: A 209 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.5868 (p90) REVERT: A 229 ARG cc_start: 0.6687 (mtt90) cc_final: 0.6378 (mmt90) REVERT: A 264 PHE cc_start: 0.7028 (p90) cc_final: 0.6787 (t80) REVERT: A 305 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8239 (mm-30) REVERT: B 388 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7353 (mttt) REVERT: B 435 GLU cc_start: 0.8207 (tp30) cc_final: 0.7858 (tp30) REVERT: B 446 LYS cc_start: 0.8222 (tppt) cc_final: 0.7887 (mttt) REVERT: E 36 TRP cc_start: 0.8454 (m100) cc_final: 0.8033 (m100) REVERT: E 106 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7356 (mp) REVERT: F 47 LEU cc_start: 0.7858 (pt) cc_final: 0.7577 (pp) REVERT: G 7 ILE cc_start: 0.5276 (OUTLIER) cc_final: 0.5030 (pt) REVERT: G 209 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5187 (p90) REVERT: G 229 ARG cc_start: 0.7240 (ptt-90) cc_final: 0.6256 (mtt90) REVERT: G 238 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7000 (mm-30) REVERT: I 348 VAL cc_start: 0.7922 (m) cc_final: 0.7571 (t) REVERT: I 435 GLU cc_start: 0.8251 (tp30) cc_final: 0.7924 (tp30) REVERT: I 446 LYS cc_start: 0.8257 (mttt) cc_final: 0.7977 (tppt) REVERT: I 494 GLU cc_start: 0.7760 (pm20) cc_final: 0.7315 (pm20) REVERT: K 27 HIS cc_start: 0.5233 (t-170) cc_final: 0.4986 (t-170) REVERT: K 79 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5466 (mp0) outliers start: 56 outliers final: 33 residues processed: 350 average time/residue: 0.1303 time to fit residues: 69.7778 Evaluate side-chains 338 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 79 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 39 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 484 ASN K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.143051 restraints weight = 24872.253| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.69 r_work: 0.3686 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17862 Z= 0.175 Angle : 0.688 10.214 24264 Z= 0.345 Chirality : 0.046 0.415 2654 Planarity : 0.004 0.048 3105 Dihedral : 5.236 57.786 2669 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 2.95 % Allowed : 15.11 % Favored : 81.94 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2163 helix: 1.04 (0.27), residues: 357 sheet: 0.45 (0.24), residues: 453 loop : -0.54 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 436 TYR 0.023 0.002 TYR C 232 PHE 0.039 0.002 PHE C 147 TRP 0.037 0.002 TRP K 35 HIS 0.008 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00408 (17826) covalent geometry : angle 0.67284 (24180) SS BOND : bond 0.00398 ( 21) SS BOND : angle 2.53083 ( 42) hydrogen bonds : bond 0.04624 ( 657) hydrogen bonds : angle 5.53659 ( 1731) Misc. bond : bond 0.00062 ( 1) link_NAG-ASN : bond 0.00438 ( 14) link_NAG-ASN : angle 2.50304 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6810 (p90) REVERT: C 209 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.5237 (p90) REVERT: C 229 ARG cc_start: 0.7417 (ptt-90) cc_final: 0.6207 (mtt90) REVERT: C 264 PHE cc_start: 0.6834 (p90) cc_final: 0.6601 (t80) REVERT: D 364 TYR cc_start: 0.6981 (m-10) cc_final: 0.6726 (m-10) REVERT: D 407 MET cc_start: 0.8057 (ttm) cc_final: 0.7606 (ttm) REVERT: D 446 LYS cc_start: 0.8272 (tppt) cc_final: 0.7757 (mttt) REVERT: D 456 LEU cc_start: 0.7454 (mt) cc_final: 0.6729 (tp) REVERT: D 474 CYS cc_start: 0.2333 (m) cc_final: 0.2016 (m) REVERT: H 30 ARG cc_start: 0.6638 (ptm-80) cc_final: 0.5712 (mpp-170) REVERT: H 32 PHE cc_start: 0.7586 (m-10) cc_final: 0.7200 (m-10) REVERT: A 209 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.5556 (p90) REVERT: A 264 PHE cc_start: 0.7070 (p90) cc_final: 0.6827 (t80) REVERT: A 276 ASP cc_start: 0.6379 (p0) cc_final: 0.5989 (p0) REVERT: A 305 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: B 364 TYR cc_start: 0.7330 (m-10) cc_final: 0.7097 (m-10) REVERT: B 388 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7337 (mttt) REVERT: B 435 GLU cc_start: 0.8309 (tp30) cc_final: 0.7919 (tp30) REVERT: B 446 LYS cc_start: 0.8225 (tppt) cc_final: 0.7877 (mttt) REVERT: E 36 TRP cc_start: 0.8454 (m100) cc_final: 0.7984 (m100) REVERT: E 46 GLU cc_start: 0.4822 (pm20) cc_final: 0.4490 (pm20) REVERT: E 106 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7390 (mp) REVERT: F 47 LEU cc_start: 0.7879 (pt) cc_final: 0.7634 (pp) REVERT: G 7 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5001 (pt) REVERT: G 209 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5032 (p90) REVERT: G 229 ARG cc_start: 0.7354 (ptt-90) cc_final: 0.6271 (mtt90) REVERT: G 238 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6991 (mm-30) REVERT: I 435 GLU cc_start: 0.8349 (tp30) cc_final: 0.8029 (tp30) REVERT: I 446 LYS cc_start: 0.8200 (mttt) cc_final: 0.7926 (tppt) REVERT: I 494 GLU cc_start: 0.7807 (pm20) cc_final: 0.7410 (pm20) REVERT: J 38 ARG cc_start: 0.6377 (ttp-170) cc_final: 0.6045 (ttp-170) REVERT: K 79 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5283 (mp0) outliers start: 56 outliers final: 39 residues processed: 332 average time/residue: 0.1445 time to fit residues: 73.1516 Evaluate side-chains 327 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 356 HIS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 79 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.185652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.143196 restraints weight = 25015.689| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.66 r_work: 0.3699 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17862 Z= 0.165 Angle : 0.684 10.436 24264 Z= 0.343 Chirality : 0.046 0.400 2654 Planarity : 0.004 0.048 3105 Dihedral : 5.213 55.980 2669 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 3.11 % Allowed : 15.48 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.18), residues: 2163 helix: 1.34 (0.27), residues: 339 sheet: 0.57 (0.26), residues: 414 loop : -0.52 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 436 TYR 0.027 0.002 TYR C 11 PHE 0.035 0.002 PHE C 147 TRP 0.032 0.002 TRP K 35 HIS 0.006 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00384 (17826) covalent geometry : angle 0.66993 (24180) SS BOND : bond 0.00369 ( 21) SS BOND : angle 2.47453 ( 42) hydrogen bonds : bond 0.04597 ( 657) hydrogen bonds : angle 5.52189 ( 1731) Misc. bond : bond 0.00057 ( 1) link_NAG-ASN : bond 0.00430 ( 14) link_NAG-ASN : angle 2.42610 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.3246 (p90) REVERT: C 229 ARG cc_start: 0.7391 (ptt-90) cc_final: 0.6179 (mtt90) REVERT: D 407 MET cc_start: 0.8016 (ttm) cc_final: 0.7685 (ttm) REVERT: D 446 LYS cc_start: 0.8227 (tppt) cc_final: 0.7799 (mttt) REVERT: D 474 CYS cc_start: 0.2351 (m) cc_final: 0.2040 (m) REVERT: H 30 ARG cc_start: 0.6774 (ptm-80) cc_final: 0.5876 (mtp180) REVERT: H 32 PHE cc_start: 0.7567 (m-10) cc_final: 0.7196 (m-10) REVERT: A 209 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.5601 (p90) REVERT: A 220 ARG cc_start: 0.6892 (mtp-110) cc_final: 0.5442 (mtt90) REVERT: A 264 PHE cc_start: 0.7106 (p90) cc_final: 0.6872 (t80) REVERT: A 305 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: B 388 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7328 (mttt) REVERT: B 435 GLU cc_start: 0.8300 (tp30) cc_final: 0.7928 (tp30) REVERT: B 446 LYS cc_start: 0.8206 (tppt) cc_final: 0.7873 (mttt) REVERT: E 36 TRP cc_start: 0.8466 (m100) cc_final: 0.8012 (m100) REVERT: E 46 GLU cc_start: 0.4813 (pm20) cc_final: 0.4476 (pm20) REVERT: E 75 SER cc_start: 0.6979 (m) cc_final: 0.6692 (p) REVERT: E 106 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7238 (mp) REVERT: F 47 LEU cc_start: 0.7884 (pt) cc_final: 0.7643 (pp) REVERT: G 7 ILE cc_start: 0.5370 (OUTLIER) cc_final: 0.4995 (pt) REVERT: G 209 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.5273 (p90) REVERT: G 229 ARG cc_start: 0.7353 (ptt-90) cc_final: 0.6269 (mtt90) REVERT: G 238 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6978 (mm-30) REVERT: I 399 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7758 (mt-10) REVERT: I 435 GLU cc_start: 0.8341 (tp30) cc_final: 0.8082 (tp30) REVERT: I 494 GLU cc_start: 0.7802 (pm20) cc_final: 0.7430 (pm20) REVERT: J 38 ARG cc_start: 0.6390 (ttp-170) cc_final: 0.6086 (ttp-170) REVERT: J 75 SER cc_start: 0.6317 (m) cc_final: 0.5694 (p) REVERT: K 79 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.5247 (mp0) outliers start: 59 outliers final: 42 residues processed: 329 average time/residue: 0.1313 time to fit residues: 65.0620 Evaluate side-chains 330 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 356 HIS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 355 HIS Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.187402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152259 restraints weight = 24864.333| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.44 r_work: 0.3662 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17862 Z= 0.139 Angle : 0.668 10.315 24264 Z= 0.333 Chirality : 0.045 0.382 2654 Planarity : 0.004 0.047 3105 Dihedral : 5.087 45.337 2667 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 2.32 % Allowed : 16.01 % Favored : 81.67 % 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 aren not related in a simple way. whole: 0.06 (0.18), residues: 2163 helix: 1.47 (0.27), residues: 339 sheet: 0.68 (0.26), residues: 399 loop : -0.50 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 101 TYR 0.019 0.002 TYR C 11 PHE 0.037 0.002 PHE C 147 TRP 0.031 0.002 TRP K 35 HIS 0.004 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00320 (17826) covalent geometry : angle 0.65465 (24180) SS BOND : bond 0.00338 ( 21) SS BOND : angle 2.32115 ( 42) hydrogen bonds : bond 0.04398 ( 657) hydrogen bonds : angle 5.38047 ( 1731) Misc. bond : bond 0.00061 ( 1) link_NAG-ASN : bond 0.00417 ( 14) link_NAG-ASN : angle 2.43728 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.2799 (p90) REVERT: C 229 ARG cc_start: 0.7237 (ptt-90) cc_final: 0.6198 (mtt90) REVERT: C 279 ASP cc_start: 0.6901 (m-30) cc_final: 0.6445 (m-30) REVERT: D 348 VAL cc_start: 0.7810 (m) cc_final: 0.7373 (t) REVERT: D 407 MET cc_start: 0.7846 (ttm) cc_final: 0.7343 (ttm) REVERT: D 446 LYS cc_start: 0.8169 (tppt) cc_final: 0.7839 (mttt) REVERT: D 474 CYS cc_start: 0.2451 (m) cc_final: 0.2120 (m) REVERT: H 30 ARG cc_start: 0.6594 (ptm-80) cc_final: 0.5838 (mtp180) REVERT: H 32 PHE cc_start: 0.7565 (m-10) cc_final: 0.7327 (m-10) REVERT: H 38 ARG cc_start: 0.6642 (ttp80) cc_final: 0.6222 (ttp-170) REVERT: H 61 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: H 85 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5639 (pp20) REVERT: L 30 ASN cc_start: 0.5950 (t0) cc_final: 0.5733 (t0) REVERT: A 209 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.5976 (p90) REVERT: A 220 ARG cc_start: 0.6817 (mtp-110) cc_final: 0.5505 (mtt90) REVERT: A 276 ASP cc_start: 0.6594 (p0) cc_final: 0.6055 (p0) REVERT: A 305 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: B 388 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7391 (mttt) REVERT: B 435 GLU cc_start: 0.8160 (tp30) cc_final: 0.7854 (tp30) REVERT: B 491 LYS cc_start: 0.8992 (tptt) cc_final: 0.8513 (ptmm) REVERT: E 36 TRP cc_start: 0.8475 (m100) cc_final: 0.8153 (m100) REVERT: E 106 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7768 (mp) REVERT: F 47 LEU cc_start: 0.7870 (pt) cc_final: 0.7621 (pp) REVERT: G 7 ILE cc_start: 0.5412 (OUTLIER) cc_final: 0.5069 (pt) REVERT: G 209 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5357 (p90) REVERT: G 229 ARG cc_start: 0.7109 (ptt-90) cc_final: 0.6183 (mtt90) REVERT: G 238 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6996 (mm-30) REVERT: I 399 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7627 (mt-10) REVERT: I 494 GLU cc_start: 0.7681 (pm20) cc_final: 0.7314 (pm20) REVERT: K 24 ARG cc_start: 0.6023 (mmp80) cc_final: 0.5819 (mmp80) REVERT: K 27 HIS cc_start: 0.4941 (t-170) cc_final: 0.4634 (t-170) REVERT: K 79 GLU cc_start: 0.5731 (mp0) cc_final: 0.5474 (mp0) outliers start: 44 outliers final: 33 residues processed: 309 average time/residue: 0.1270 time to fit residues: 59.9895 Evaluate side-chains 315 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain I residue 355 HIS Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 195 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 HIS A 32 HIS A 68 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 GLN J 6 GLN ** K 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 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 = 0.4322 r_free = 0.4322 target = 0.181396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132724 restraints weight = 25081.211| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.30 r_work: 0.3620 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 17862 Z= 0.293 Angle : 0.812 10.760 24264 Z= 0.412 Chirality : 0.050 0.384 2654 Planarity : 0.006 0.083 3105 Dihedral : 5.828 40.254 2667 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.17 % Rotamer: Outliers : 2.84 % Allowed : 15.69 % Favored : 81.46 % 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 aren not related in a simple way. whole: -0.48 (0.18), residues: 2163 helix: 0.45 (0.26), residues: 363 sheet: 0.55 (0.27), residues: 405 loop : -0.81 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.024 0.003 TYR C 232 PHE 0.056 0.003 PHE C 147 TRP 0.043 0.003 TRP B 351 HIS 0.013 0.002 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00688 (17826) covalent geometry : angle 0.79577 (24180) SS BOND : bond 0.00622 ( 21) SS BOND : angle 2.48184 ( 42) hydrogen bonds : bond 0.05178 ( 657) hydrogen bonds : angle 6.00791 ( 1731) Misc. bond : bond 0.00059 ( 1) link_NAG-ASN : bond 0.00520 ( 14) link_NAG-ASN : angle 3.25042 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5830.15 seconds wall clock time: 100 minutes 19.17 seconds (6019.17 seconds total)