Starting phenix.real_space_refine on Sun Jun 15 13:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2m_44112/06_2025/9b2m_44112.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2m_44112/06_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_44112/06_2025/9b2m_44112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2m_44112/06_2025/9b2m_44112.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2m_44112/06_2025/9b2m_44112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2m_44112/06_2025/9b2m_44112.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.99, per 1000 atoms: 0.63 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: 4.00 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.83 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: 6.16 Time building geometry restraints manager: 4.85 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: 0.05 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: 2.720 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.600 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (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 TRP 0.038 0.009 TRP J 47 HIS 0.012 0.003 HIS D 472 PHE 0.063 0.009 PHE G 115 TYR 0.058 0.010 TYR B 471 ARG 0.009 0.001 ARG C 229 Details of bonding type rmsd link_NAG-ASN : bond 0.08353 ( 14) link_NAG-ASN : angle 2.98003 ( 42) hydrogen bonds : bond 0.16089 ( 657) hydrogen bonds : angle 7.67178 ( 1731) SS BOND : bond 0.05638 ( 21) SS BOND : angle 3.78007 ( 42) covalent geometry : bond 0.02254 (17826) covalent geometry : angle 1.90737 (24180) Misc. bond : bond 0.22558 ( 1) *********************** 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 : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 396 VAL cc_start: 0.7729 (t) cc_final: 0.7458 (p) REVERT: L 79 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5029 (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: 0.5684 (mm-30) REVERT: I 484 ASN cc_start: 0.4921 (m-40) cc_final: 0.4714 (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: 0.5683 (mp0) outliers start: 5 outliers final: 2 residues processed: 511 average time/residue: 0.3103 time to fit residues: 236.2157 Evaluate side-chains 301 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 297 time to evaluate : 2.840 ------------------------------------------------------------------------------- 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 179 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 HIS C 187 ASN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.191258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.150392 restraints weight = 25320.067| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.62 r_work: 0.3807 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17862 Z= 0.191 Angle : 0.732 10.611 24264 Z= 0.380 Chirality : 0.047 0.206 2654 Planarity : 0.005 0.044 3105 Dihedral : 6.140 45.980 2675 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.00 % Allowed : 8.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2163 helix: 0.72 (0.26), residues: 360 sheet: 1.06 (0.24), residues: 468 loop : -0.15 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 105 HIS 0.008 0.002 HIS G 184 PHE 0.031 0.003 PHE H 103 TYR 0.019 0.002 TYR H 79 ARG 0.007 0.001 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 14) link_NAG-ASN : angle 2.32425 ( 42) hydrogen bonds : bond 0.05523 ( 657) hydrogen bonds : angle 6.01020 ( 1731) SS BOND : bond 0.00978 ( 21) SS BOND : angle 1.50755 ( 42) covalent geometry : bond 0.00415 (17826) covalent geometry : angle 0.72387 (24180) Misc. bond : bond 0.00118 ( 1) *********************** 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 441 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 384 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7698 (ptmt) REVERT: C 229 ARG cc_start: 0.7490 (ptt-90) cc_final: 0.6380 (mtt90) REVERT: C 264 PHE cc_start: 0.6709 (p90) cc_final: 0.6268 (t80) REVERT: C 276 ASP cc_start: 0.6553 (p0) cc_final: 0.6175 (p0) REVERT: D 396 VAL cc_start: 0.7884 (t) cc_final: 0.7605 (p) REVERT: D 407 MET cc_start: 0.8053 (ttm) cc_final: 0.7536 (ttm) REVERT: D 446 LYS cc_start: 0.8135 (tppt) cc_final: 0.7807 (mttt) REVERT: D 474 CYS cc_start: 0.3219 (m) cc_final: 0.2947 (m) REVERT: L 79 GLU cc_start: 0.5839 (mt-10) cc_final: 0.5572 (mp0) REVERT: A 264 PHE cc_start: 0.6994 (p90) cc_final: 0.6348 (t80) REVERT: B 347 MET cc_start: 0.6359 (ttp) cc_final: 0.6080 (ttp) REVERT: B 407 MET cc_start: 0.7614 (tpp) cc_final: 0.7318 (ttm) REVERT: B 435 GLU cc_start: 0.8052 (tp30) cc_final: 0.7831 (tp30) REVERT: E 48 MET cc_start: 0.8428 (mmm) cc_final: 0.8159 (mmt) REVERT: E 106 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7459 (mp) REVERT: G 51 ILE cc_start: 0.8068 (mp) cc_final: 0.7749 (tp) REVERT: G 229 ARG cc_start: 0.7343 (ptt-90) cc_final: 0.6278 (mtt90) REVERT: G 264 PHE cc_start: 0.6760 (p90) cc_final: 0.6326 (t80) REVERT: I 488 ASP cc_start: 0.7747 (p0) cc_final: 0.7478 (p0) REVERT: J 81 GLU cc_start: 0.7751 (mp0) cc_final: 0.7515 (mm-30) REVERT: K 35 TRP cc_start: 0.6353 (m100) cc_final: 0.5973 (m100) outliers start: 57 outliers final: 27 residues processed: 417 average time/residue: 0.3138 time to fit residues: 195.5171 Evaluate side-chains 327 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 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 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 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 34 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 I 409 ASN I 455 GLN ** I 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 58 ASN K 30 ASN K 38 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.189025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142836 restraints weight = 25143.214| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.33 r_work: 0.3770 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17862 Z= 0.169 Angle : 0.678 14.814 24264 Z= 0.347 Chirality : 0.047 0.523 2654 Planarity : 0.005 0.048 3105 Dihedral : 5.740 57.368 2669 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.79 % Allowed : 10.64 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2163 helix: 0.56 (0.26), residues: 375 sheet: 0.84 (0.24), residues: 468 loop : -0.35 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 36 HIS 0.007 0.001 HIS G 184 PHE 0.020 0.002 PHE H 103 TYR 0.013 0.002 TYR B 492 ARG 0.009 0.001 ARG I 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 14) link_NAG-ASN : angle 3.38767 ( 42) hydrogen bonds : bond 0.04970 ( 657) hydrogen bonds : angle 5.65650 ( 1731) SS BOND : bond 0.00438 ( 21) SS BOND : angle 1.64973 ( 42) covalent geometry : bond 0.00382 (17826) covalent geometry : angle 0.66044 (24180) Misc. bond : bond 0.00065 ( 1) *********************** 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 384 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 SER cc_start: 0.8333 (m) cc_final: 0.8041 (m) REVERT: C 209 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.4231 (p90) REVERT: C 229 ARG cc_start: 0.7392 (ptt-90) cc_final: 0.6258 (mtt90) REVERT: C 245 PHE cc_start: 0.7757 (t80) cc_final: 0.6474 (t80) REVERT: C 264 PHE cc_start: 0.6782 (p90) cc_final: 0.6447 (t80) REVERT: D 407 MET cc_start: 0.7991 (ttm) cc_final: 0.7640 (ttm) REVERT: D 446 LYS cc_start: 0.8146 (tppt) cc_final: 0.7837 (mttt) REVERT: D 474 CYS cc_start: 0.2892 (m) cc_final: 0.2640 (m) REVERT: L 79 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5822 (mp0) REVERT: A 209 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5379 (p90) REVERT: A 264 PHE cc_start: 0.7070 (p90) cc_final: 0.6695 (t80) REVERT: B 407 MET cc_start: 0.7846 (tpp) cc_final: 0.7609 (ttm) REVERT: B 435 GLU cc_start: 0.8206 (tp30) cc_final: 0.7910 (tp30) REVERT: E 46 GLU cc_start: 0.4749 (pm20) cc_final: 0.4464 (pm20) REVERT: E 106 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7382 (mp) REVERT: G 209 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.5137 (p90) REVERT: G 229 ARG cc_start: 0.7308 (ptt-90) cc_final: 0.6314 (mtt90) REVERT: G 245 PHE cc_start: 0.7878 (t80) cc_final: 0.7156 (t80) REVERT: G 264 PHE cc_start: 0.6887 (p90) cc_final: 0.6624 (t80) REVERT: I 446 LYS cc_start: 0.8170 (tppt) cc_final: 0.7968 (mttt) REVERT: J 81 GLU cc_start: 0.7845 (mp0) cc_final: 0.7467 (mm-30) REVERT: K 30 ASN cc_start: 0.6190 (m-40) cc_final: 0.5907 (m110) REVERT: K 79 GLU cc_start: 0.6061 (mp0) cc_final: 0.5826 (mp0) outliers start: 53 outliers final: 29 residues processed: 361 average time/residue: 0.2947 time to fit residues: 159.4225 Evaluate side-chains 314 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 2.050 ------------------------------------------------------------------------------- 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 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 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 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 180 TRP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 252 ILE 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 10 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN D 476 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN F 30 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 32 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.181970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133538 restraints weight = 25067.632| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.32 r_work: 0.3648 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 17862 Z= 0.296 Angle : 0.806 14.073 24264 Z= 0.415 Chirality : 0.051 0.596 2654 Planarity : 0.005 0.051 3105 Dihedral : 6.176 56.180 2669 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.42 % Allowed : 11.59 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2163 helix: 0.09 (0.26), residues: 363 sheet: 0.47 (0.25), residues: 450 loop : -0.64 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 351 HIS 0.014 0.002 HIS G 184 PHE 0.031 0.003 PHE C 258 TYR 0.020 0.003 TYR A 209 ARG 0.006 0.001 ARG G 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 14) link_NAG-ASN : angle 3.64307 ( 42) hydrogen bonds : bond 0.05434 ( 657) hydrogen bonds : angle 6.06299 ( 1731) SS BOND : bond 0.00521 ( 21) SS BOND : angle 2.15255 ( 42) covalent geometry : bond 0.00690 (17826) covalent geometry : angle 0.78814 (24180) Misc. bond : bond 0.00016 ( 1) *********************** 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 370 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6891 (p-80) REVERT: C 209 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.4606 (p90) REVERT: C 229 ARG cc_start: 0.7403 (ptt-90) cc_final: 0.6360 (mtt90) REVERT: C 264 PHE cc_start: 0.6988 (p90) cc_final: 0.6651 (t80) REVERT: D 407 MET cc_start: 0.8153 (ttm) cc_final: 0.7770 (ttm) REVERT: D 475 ASN cc_start: 0.7077 (p0) cc_final: 0.6600 (p0) REVERT: A 264 PHE cc_start: 0.7124 (p90) cc_final: 0.6817 (t80) REVERT: B 435 GLU cc_start: 0.8480 (tp30) cc_final: 0.8065 (tp30) REVERT: B 446 LYS cc_start: 0.8333 (tppt) cc_final: 0.7802 (mttt) REVERT: B 494 GLU cc_start: 0.7740 (pm20) cc_final: 0.7373 (pm20) REVERT: E 36 TRP cc_start: 0.8487 (m100) cc_final: 0.7902 (m100) REVERT: E 46 GLU cc_start: 0.5027 (pm20) cc_final: 0.4648 (pm20) REVERT: E 106 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7597 (mp) REVERT: E 109 ASP cc_start: 0.7052 (t70) cc_final: 0.6743 (p0) REVERT: F 47 LEU cc_start: 0.7753 (pt) cc_final: 0.7454 (pp) REVERT: G 39 ASP cc_start: 0.8167 (p0) cc_final: 0.7885 (p0) REVERT: G 229 ARG cc_start: 0.7383 (ptt-90) cc_final: 0.6374 (mtt90) REVERT: I 435 GLU cc_start: 0.8295 (tp30) cc_final: 0.7940 (tp30) REVERT: J 36 TRP cc_start: 0.8454 (m100) cc_final: 0.8189 (m100) REVERT: K 27 HIS cc_start: 0.5415 (t-170) cc_final: 0.5142 (t-170) REVERT: K 79 GLU cc_start: 0.5616 (mp0) cc_final: 0.5374 (mp0) outliers start: 65 outliers final: 51 residues processed: 354 average time/residue: 0.2997 time to fit residues: 159.4552 Evaluate side-chains 309 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 PHE 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 219 LYS 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 106 LEU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 12 HIS 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 175 GLU 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 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 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 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 356 HIS 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 14 SER 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 141 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS C 196 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 286 GLN D 409 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN F 30 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 HIS G 286 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.186465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139219 restraints weight = 25386.113| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.31 r_work: 0.3709 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17862 Z= 0.163 Angle : 0.669 11.390 24264 Z= 0.342 Chirality : 0.046 0.476 2654 Planarity : 0.005 0.050 3105 Dihedral : 5.562 59.345 2669 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.26 % Allowed : 12.37 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2163 helix: 0.44 (0.26), residues: 375 sheet: 0.50 (0.25), residues: 450 loop : -0.67 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 35 HIS 0.006 0.001 HIS G 184 PHE 0.017 0.002 PHE G 115 TYR 0.015 0.002 TYR G 232 ARG 0.006 0.001 ARG I 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 14) link_NAG-ASN : angle 2.87147 ( 42) hydrogen bonds : bond 0.04811 ( 657) hydrogen bonds : angle 5.65027 ( 1731) SS BOND : bond 0.00423 ( 21) SS BOND : angle 2.44952 ( 42) covalent geometry : bond 0.00373 (17826) covalent geometry : angle 0.65145 (24180) Misc. bond : bond 0.00036 ( 1) *********************** 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 374 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6725 (p90) REVERT: C 209 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.5313 (p90) REVERT: C 229 ARG cc_start: 0.7429 (ptt-90) cc_final: 0.6288 (mtt90) REVERT: C 264 PHE cc_start: 0.6940 (p90) cc_final: 0.6669 (t80) REVERT: D 407 MET cc_start: 0.7981 (ttm) cc_final: 0.7641 (ttm) REVERT: D 446 LYS cc_start: 0.8207 (tppt) cc_final: 0.7814 (mttt) REVERT: H 36 TRP cc_start: 0.8277 (m100) cc_final: 0.7792 (m100) REVERT: L 35 TRP cc_start: 0.6930 (m100) cc_final: 0.6582 (m100) REVERT: A 209 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.5973 (p90) REVERT: A 264 PHE cc_start: 0.7157 (p90) cc_final: 0.6864 (t80) REVERT: B 388 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7445 (mttt) REVERT: B 435 GLU cc_start: 0.8346 (tp30) cc_final: 0.7951 (tp30) REVERT: B 446 LYS cc_start: 0.8230 (tppt) cc_final: 0.7784 (mttt) REVERT: B 494 GLU cc_start: 0.7794 (pm20) cc_final: 0.7567 (pm20) REVERT: E 36 TRP cc_start: 0.8384 (m100) cc_final: 0.8045 (m100) REVERT: E 38 ARG cc_start: 0.6071 (ttp-170) cc_final: 0.5803 (ttp-170) REVERT: E 106 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7446 (mp) REVERT: F 47 LEU cc_start: 0.7857 (pt) cc_final: 0.7571 (pp) REVERT: G 209 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5218 (p90) REVERT: G 229 ARG cc_start: 0.7347 (ptt-90) cc_final: 0.6260 (mtt90) REVERT: G 245 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7142 (t80) REVERT: G 276 ASP cc_start: 0.6856 (p0) cc_final: 0.6613 (p0) REVERT: I 435 GLU cc_start: 0.8318 (tp30) cc_final: 0.7951 (tp30) REVERT: I 446 LYS cc_start: 0.8083 (tppt) cc_final: 0.7838 (mttt) REVERT: J 91 TYR cc_start: 0.6114 (m-80) cc_final: 0.5864 (m-80) REVERT: K 27 HIS cc_start: 0.5473 (t-170) cc_final: 0.5265 (t-170) REVERT: K 79 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5452 (mp0) outliers start: 62 outliers final: 34 residues processed: 355 average time/residue: 0.3548 time to fit residues: 193.4948 Evaluate side-chains 329 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 51 ILE 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 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 219 LYS 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 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 12 HIS 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 208 HIS Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain E residue 106 LEU 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 146 SER 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 368 GLN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 79 GLU 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 63 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 202 optimal weight: 0.2980 chunk 159 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** B 380 ASN F 30 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 32 HIS G 208 HIS ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.187255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140859 restraints weight = 25285.447| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.60 r_work: 0.3702 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17862 Z= 0.152 Angle : 0.650 10.540 24264 Z= 0.332 Chirality : 0.045 0.438 2654 Planarity : 0.004 0.049 3105 Dihedral : 5.353 57.042 2669 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.16 % Allowed : 13.06 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2163 helix: 0.65 (0.27), residues: 375 sheet: 0.49 (0.25), residues: 420 loop : -0.61 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 35 HIS 0.017 0.001 HIS C 12 PHE 0.017 0.002 PHE G 115 TYR 0.029 0.002 TYR C 11 ARG 0.006 0.001 ARG D 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 14) link_NAG-ASN : angle 2.64407 ( 42) hydrogen bonds : bond 0.04626 ( 657) hydrogen bonds : angle 5.54052 ( 1731) SS BOND : bond 0.00336 ( 21) SS BOND : angle 2.14388 ( 42) covalent geometry : bond 0.00348 (17826) covalent geometry : angle 0.63536 (24180) Misc. bond : bond 0.00062 ( 1) *********************** 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 365 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.5167 (p90) REVERT: C 229 ARG cc_start: 0.7469 (ptt-90) cc_final: 0.6279 (mtt90) REVERT: C 264 PHE cc_start: 0.7019 (p90) cc_final: 0.6685 (t80) REVERT: D 407 MET cc_start: 0.8036 (ttm) cc_final: 0.7611 (ttm) REVERT: D 446 LYS cc_start: 0.8196 (tppt) cc_final: 0.7820 (mttt) REVERT: H 30 ARG cc_start: 0.6535 (ptm-80) cc_final: 0.5607 (mtp180) REVERT: H 79 TYR cc_start: 0.7663 (m-10) cc_final: 0.7459 (m-10) REVERT: A 209 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.5788 (p90) REVERT: A 264 PHE cc_start: 0.7227 (p90) cc_final: 0.6874 (t80) REVERT: A 277 GLU cc_start: 0.7661 (tp30) cc_final: 0.7396 (mp0) REVERT: A 305 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: B 388 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7432 (mttt) REVERT: B 407 MET cc_start: 0.7671 (ttm) cc_final: 0.7469 (ttm) REVERT: B 435 GLU cc_start: 0.8377 (tp30) cc_final: 0.8001 (tp30) REVERT: B 446 LYS cc_start: 0.8269 (tppt) cc_final: 0.7917 (mttt) REVERT: E 36 TRP cc_start: 0.8465 (m100) cc_final: 0.8025 (m100) REVERT: E 106 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7359 (mp) REVERT: F 47 LEU cc_start: 0.7872 (pt) cc_final: 0.7596 (pp) REVERT: G 7 ILE cc_start: 0.4994 (OUTLIER) cc_final: 0.4645 (pt) REVERT: G 209 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5408 (p90) REVERT: G 229 ARG cc_start: 0.7390 (ptt-90) cc_final: 0.6250 (mtt90) REVERT: G 245 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7134 (t80) REVERT: G 276 ASP cc_start: 0.6786 (p0) cc_final: 0.6465 (p0) REVERT: I 435 GLU cc_start: 0.8289 (tp30) cc_final: 0.7929 (tp30) REVERT: K 27 HIS cc_start: 0.5344 (t-170) cc_final: 0.5128 (t-170) REVERT: K 30 ASN cc_start: 0.5731 (m-40) cc_final: 0.5505 (m110) REVERT: K 79 GLU cc_start: 0.5764 (OUTLIER) cc_final: 0.5513 (mp0) outliers start: 60 outliers final: 36 residues processed: 346 average time/residue: 0.2782 time to fit residues: 146.3976 Evaluate side-chains 318 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 219 LYS 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 77 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 SER 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 305 GLU 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 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 146 SER 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 368 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 79 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 197 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4334 r_free = 0.4334 target = 0.182285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134551 restraints weight = 24895.133| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.36 r_work: 0.3629 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17862 Z= 0.245 Angle : 0.752 10.151 24264 Z= 0.384 Chirality : 0.048 0.419 2654 Planarity : 0.005 0.050 3105 Dihedral : 5.787 53.472 2669 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.48 % Allowed : 13.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2163 helix: 0.37 (0.26), residues: 378 sheet: 0.51 (0.26), residues: 396 loop : -0.79 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 351 HIS 0.012 0.002 HIS C 184 PHE 0.023 0.003 PHE A 115 TYR 0.031 0.002 TYR C 11 ARG 0.006 0.001 ARG I 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 14) link_NAG-ASN : angle 2.88083 ( 42) hydrogen bonds : bond 0.05042 ( 657) hydrogen bonds : angle 5.87392 ( 1731) SS BOND : bond 0.00509 ( 21) SS BOND : angle 2.82423 ( 42) covalent geometry : bond 0.00575 (17826) covalent geometry : angle 0.73380 (24180) Misc. bond : bond 0.00033 ( 1) *********************** 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 361 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.4615 (p90) REVERT: C 229 ARG cc_start: 0.7596 (ptt-90) cc_final: 0.6337 (mmm-85) REVERT: C 276 ASP cc_start: 0.6462 (p0) cc_final: 0.6125 (p0) REVERT: D 407 MET cc_start: 0.8104 (ttm) cc_final: 0.7677 (ttm) REVERT: D 446 LYS cc_start: 0.8265 (tppt) cc_final: 0.7843 (mttt) REVERT: D 457 LYS cc_start: 0.7495 (ptmm) cc_final: 0.7202 (mmmt) REVERT: H 38 ARG cc_start: 0.6774 (ttp-170) cc_final: 0.6298 (ttp-170) REVERT: H 79 TYR cc_start: 0.7699 (m-10) cc_final: 0.7499 (m-10) REVERT: A 264 PHE cc_start: 0.7273 (p90) cc_final: 0.7005 (t80) REVERT: A 276 ASP cc_start: 0.7054 (p0) cc_final: 0.6307 (p0) REVERT: A 305 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: B 388 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7491 (mttt) REVERT: B 435 GLU cc_start: 0.8437 (tp30) cc_final: 0.7986 (tp30) REVERT: B 446 LYS cc_start: 0.8223 (tppt) cc_final: 0.7887 (mttt) REVERT: B 479 MET cc_start: 0.7264 (mmp) cc_final: 0.6903 (mmp) REVERT: E 36 TRP cc_start: 0.8443 (m100) cc_final: 0.7866 (m100) REVERT: E 46 GLU cc_start: 0.5022 (pm20) cc_final: 0.4532 (pm20) REVERT: E 106 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7424 (mp) REVERT: F 47 LEU cc_start: 0.7880 (pt) cc_final: 0.7656 (pp) REVERT: G 209 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.4771 (p90) REVERT: G 229 ARG cc_start: 0.7464 (ptt-90) cc_final: 0.6291 (mtt90) REVERT: G 276 ASP cc_start: 0.7082 (p0) cc_final: 0.6826 (p0) REVERT: I 435 GLU cc_start: 0.8426 (tp30) cc_final: 0.7985 (tp30) REVERT: I 457 LYS cc_start: 0.7560 (pttt) cc_final: 0.7358 (ttmm) REVERT: K 79 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.5359 (mp0) outliers start: 66 outliers final: 52 residues processed: 343 average time/residue: 0.2942 time to fit residues: 151.6806 Evaluate side-chains 330 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain D residue 348 VAL 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 77 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 12 HIS 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 345 THR 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 B residue 476 ASN Chi-restraints excluded: chain E residue 106 LEU 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 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 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 245 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 355 HIS Chi-restraints excluded: chain I residue 356 HIS Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.185354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137667 restraints weight = 24964.627| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.30 r_work: 0.3693 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6167 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= 0.171 Angle : 0.695 10.032 24264 Z= 0.352 Chirality : 0.046 0.401 2654 Planarity : 0.005 0.054 3105 Dihedral : 5.540 55.712 2667 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 14.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2163 helix: 0.76 (0.27), residues: 360 sheet: 0.63 (0.26), residues: 396 loop : -0.77 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 351 HIS 0.009 0.001 HIS C 12 PHE 0.017 0.002 PHE G 115 TYR 0.026 0.002 TYR C 11 ARG 0.009 0.001 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 14) link_NAG-ASN : angle 2.97576 ( 42) hydrogen bonds : bond 0.04745 ( 657) hydrogen bonds : angle 5.65993 ( 1731) SS BOND : bond 0.00349 ( 21) SS BOND : angle 2.59209 ( 42) covalent geometry : bond 0.00396 (17826) covalent geometry : angle 0.67683 (24180) Misc. bond : bond 0.00030 ( 1) *********************** 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 354 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.4981 (p90) REVERT: C 229 ARG cc_start: 0.7550 (ptt-90) cc_final: 0.6338 (mmm-85) REVERT: C 245 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7272 (t80) REVERT: D 407 MET cc_start: 0.7994 (ttm) cc_final: 0.7493 (ttm) REVERT: D 446 LYS cc_start: 0.8281 (tppt) cc_final: 0.7864 (mttt) REVERT: D 457 LYS cc_start: 0.7501 (ptmm) cc_final: 0.7204 (mtmt) REVERT: H 30 ARG cc_start: 0.6515 (ptm-80) cc_final: 0.5755 (mtp180) REVERT: H 36 TRP cc_start: 0.8309 (m100) cc_final: 0.7843 (m100) REVERT: H 61 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8417 (mt0) REVERT: A 264 PHE cc_start: 0.7148 (p90) cc_final: 0.6914 (t80) REVERT: A 276 ASP cc_start: 0.6548 (p0) cc_final: 0.6155 (p0) REVERT: A 305 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: B 388 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7601 (mttt) REVERT: B 435 GLU cc_start: 0.8388 (tp30) cc_final: 0.7939 (tp30) REVERT: B 446 LYS cc_start: 0.8290 (tppt) cc_final: 0.7905 (mttt) REVERT: E 36 TRP cc_start: 0.8477 (m100) cc_final: 0.7998 (m100) REVERT: E 46 GLU cc_start: 0.5045 (pm20) cc_final: 0.4640 (pm20) REVERT: E 106 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7577 (mp) REVERT: F 47 LEU cc_start: 0.7889 (pt) cc_final: 0.7656 (pp) REVERT: G 209 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.5174 (p90) REVERT: G 229 ARG cc_start: 0.7365 (ptt-90) cc_final: 0.6266 (mtt90) REVERT: G 245 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7211 (t80) REVERT: G 276 ASP cc_start: 0.7008 (p0) cc_final: 0.6756 (p0) REVERT: I 348 VAL cc_start: 0.7847 (m) cc_final: 0.7590 (t) REVERT: I 435 GLU cc_start: 0.8378 (tp30) cc_final: 0.8061 (tp30) REVERT: K 79 GLU cc_start: 0.5708 (mp0) cc_final: 0.5367 (mp0) outliers start: 57 outliers final: 41 residues processed: 336 average time/residue: 0.3117 time to fit residues: 159.4982 Evaluate side-chains 326 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 PHE 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 219 LYS Chi-restraints excluded: chain C residue 245 PHE 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 77 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain A residue 6 THR 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 209 TYR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 352 TYR 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 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 245 PHE 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 K residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 90 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 121 optimal weight: 0.1980 chunk 179 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** 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 12 HIS ** 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** I 357 GLN ** K 34 HIS ** 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 = 0.4326 r_free = 0.4326 target = 0.181625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134430 restraints weight = 25023.623| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.61 r_work: 0.3606 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 17862 Z= 0.251 Angle : 0.771 11.375 24264 Z= 0.393 Chirality : 0.049 0.389 2654 Planarity : 0.005 0.052 3105 Dihedral : 5.810 43.126 2667 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.16 % Allowed : 14.69 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2163 helix: 0.46 (0.27), residues: 360 sheet: 0.46 (0.27), residues: 396 loop : -0.86 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 351 HIS 0.013 0.001 HIS C 184 PHE 0.024 0.002 PHE G 115 TYR 0.020 0.002 TYR G 232 ARG 0.007 0.001 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 14) link_NAG-ASN : angle 3.13183 ( 42) hydrogen bonds : bond 0.05092 ( 657) hydrogen bonds : angle 5.97877 ( 1731) SS BOND : bond 0.00473 ( 21) SS BOND : angle 2.58246 ( 42) covalent geometry : bond 0.00588 (17826) covalent geometry : angle 0.75409 (24180) Misc. bond : bond 0.00049 ( 1) *********************** 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 339 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.4550 (p90) REVERT: C 229 ARG cc_start: 0.7618 (ptt-90) cc_final: 0.6363 (mmm-85) REVERT: D 407 MET cc_start: 0.8184 (ttm) cc_final: 0.7797 (ttm) REVERT: D 457 LYS cc_start: 0.7516 (ptmm) cc_final: 0.7229 (mmmt) REVERT: D 482 VAL cc_start: 0.8350 (t) cc_final: 0.8147 (p) REVERT: A 264 PHE cc_start: 0.7362 (p90) cc_final: 0.7044 (t80) REVERT: A 276 ASP cc_start: 0.6603 (p0) cc_final: 0.6153 (p0) REVERT: A 305 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: B 388 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7495 (mttt) REVERT: B 435 GLU cc_start: 0.8498 (tp30) cc_final: 0.7984 (tp30) REVERT: B 446 LYS cc_start: 0.8260 (tppt) cc_final: 0.7900 (mttt) REVERT: B 488 ASP cc_start: 0.7496 (p0) cc_final: 0.7227 (t0) REVERT: B 491 LYS cc_start: 0.9059 (tptt) cc_final: 0.8550 (pttm) REVERT: E 36 TRP cc_start: 0.8458 (m100) cc_final: 0.7838 (m100) REVERT: E 38 ARG cc_start: 0.6442 (ttp-170) cc_final: 0.6172 (ttp-170) REVERT: E 46 GLU cc_start: 0.5236 (pm20) cc_final: 0.4888 (pm20) REVERT: E 48 MET cc_start: 0.8261 (mmt) cc_final: 0.7843 (mmt) REVERT: E 79 TYR cc_start: 0.7644 (m-10) cc_final: 0.7256 (m-10) REVERT: E 106 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7485 (mp) REVERT: F 47 LEU cc_start: 0.7879 (pt) cc_final: 0.7672 (pp) REVERT: G 229 ARG cc_start: 0.7473 (ptt-90) cc_final: 0.6291 (mtt90) REVERT: G 258 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.5545 (p90) REVERT: G 276 ASP cc_start: 0.7250 (p0) cc_final: 0.6975 (p0) REVERT: I 348 VAL cc_start: 0.8092 (m) cc_final: 0.7885 (t) REVERT: I 435 GLU cc_start: 0.8477 (tp30) cc_final: 0.8039 (tp30) REVERT: J 38 ARG cc_start: 0.6496 (ttp-170) cc_final: 0.6043 (ttp80) REVERT: J 48 MET cc_start: 0.8453 (mmm) cc_final: 0.8240 (mmt) REVERT: K 79 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5408 (mp0) outliers start: 60 outliers final: 43 residues processed: 321 average time/residue: 0.2911 time to fit residues: 142.1792 Evaluate side-chains 321 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 51 ILE 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 219 LYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain D residue 348 VAL 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 77 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 6 THR 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 209 TYR Chi-restraints excluded: chain A residue 305 GLU 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 14 SER Chi-restraints excluded: chain F residue 46 LEU 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 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 245 PHE Chi-restraints excluded: chain G residue 258 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 355 HIS Chi-restraints excluded: chain I residue 356 HIS 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 24 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 198 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS L 90 GLN A 32 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN I 357 GLN ** 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 = 0.4370 r_free = 0.4370 target = 0.186331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144672 restraints weight = 24955.618| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.43 r_work: 0.3684 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17862 Z= 0.149 Angle : 0.682 10.089 24264 Z= 0.345 Chirality : 0.046 0.374 2654 Planarity : 0.005 0.049 3105 Dihedral : 5.346 40.128 2667 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.42 % Allowed : 15.53 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2163 helix: 1.21 (0.27), residues: 339 sheet: 0.55 (0.27), residues: 402 loop : -0.70 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 351 HIS 0.008 0.001 HIS K 34 PHE 0.020 0.002 PHE A 147 TYR 0.018 0.002 TYR A 11 ARG 0.006 0.001 ARG D 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 14) link_NAG-ASN : angle 2.59022 ( 42) hydrogen bonds : bond 0.04642 ( 657) hydrogen bonds : angle 5.62394 ( 1731) SS BOND : bond 0.00319 ( 21) SS BOND : angle 2.41182 ( 42) covalent geometry : bond 0.00342 (17826) covalent geometry : angle 0.66723 (24180) Misc. bond : bond 0.00054 ( 1) ********************** 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 351 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5273 (p90) REVERT: C 229 ARG cc_start: 0.7581 (ptt-90) cc_final: 0.6334 (mmm-85) REVERT: D 407 MET cc_start: 0.7997 (ttm) cc_final: 0.7513 (ttm) REVERT: D 446 LYS cc_start: 0.8215 (tppt) cc_final: 0.7870 (mttt) REVERT: D 457 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7226 (mtmt) REVERT: H 30 ARG cc_start: 0.6590 (ptm-80) cc_final: 0.6220 (mpp-170) REVERT: H 36 TRP cc_start: 0.8288 (m100) cc_final: 0.7888 (m100) REVERT: H 38 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.6459 (ttp-170) REVERT: A 209 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.5750 (p90) REVERT: A 264 PHE cc_start: 0.7247 (p90) cc_final: 0.6968 (t80) REVERT: A 276 ASP cc_start: 0.6407 (p0) cc_final: 0.5984 (p0) REVERT: A 305 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: B 388 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7479 (mttt) REVERT: B 435 GLU cc_start: 0.8372 (tp30) cc_final: 0.7934 (tp30) REVERT: B 446 LYS cc_start: 0.8306 (tppt) cc_final: 0.7958 (mttt) REVERT: B 488 ASP cc_start: 0.7575 (p0) cc_final: 0.7237 (t0) REVERT: B 491 LYS cc_start: 0.9039 (tptt) cc_final: 0.8507 (pttm) REVERT: E 36 TRP cc_start: 0.8420 (m100) cc_final: 0.7997 (m100) REVERT: E 46 GLU cc_start: 0.5157 (pm20) cc_final: 0.4837 (pm20) REVERT: E 75 SER cc_start: 0.6891 (m) cc_final: 0.6639 (p) REVERT: E 106 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7484 (mp) REVERT: F 47 LEU cc_start: 0.7871 (pt) cc_final: 0.7644 (pp) REVERT: G 160 LEU cc_start: 0.7574 (pp) cc_final: 0.7056 (mt) REVERT: G 209 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5289 (p90) REVERT: G 229 ARG cc_start: 0.7379 (ptt-90) cc_final: 0.6281 (mtt90) REVERT: G 245 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7143 (t80) REVERT: I 435 GLU cc_start: 0.8398 (tp30) cc_final: 0.8189 (tp30) REVERT: I 474 CYS cc_start: 0.2376 (m) cc_final: 0.1741 (m) REVERT: I 486 THR cc_start: 0.8167 (p) cc_final: 0.7937 (t) REVERT: J 38 ARG cc_start: 0.6214 (ttp-170) cc_final: 0.5908 (ttp80) REVERT: K 79 GLU cc_start: 0.5811 (mp0) cc_final: 0.5464 (mp0) outliers start: 46 outliers final: 36 residues processed: 335 average time/residue: 0.4012 time to fit residues: 209.1124 Evaluate side-chains 332 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 51 ILE 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 219 LYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 6 THR 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 209 TYR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 352 TYR 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 85 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 118 PHE 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 188 ILE Chi-restraints excluded: chain G residue 209 TYR Chi-restraints excluded: chain G residue 245 PHE Chi-restraints excluded: chain I residue 355 HIS Chi-restraints excluded: chain I residue 368 GLN 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 209 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 0.0170 chunk 24 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 174 optimal weight: 0.0050 overall best weight: 0.3432 ------------------------------------------------------------------------------- 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** D 401 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.189017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144687 restraints weight = 25112.194| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.49 r_work: 0.3750 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17862 Z= 0.124 Angle : 0.653 10.983 24264 Z= 0.328 Chirality : 0.045 0.355 2654 Planarity : 0.005 0.048 3105 Dihedral : 4.984 36.979 2667 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.21 % Allowed : 15.90 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2163 helix: 1.48 (0.28), residues: 339 sheet: 0.73 (0.27), residues: 399 loop : -0.66 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.006 0.001 HIS L 34 PHE 0.020 0.002 PHE A 147 TYR 0.020 0.002 TYR I 489 ARG 0.006 0.001 ARG D 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 14) link_NAG-ASN : angle 2.28298 ( 42) hydrogen bonds : bond 0.04299 ( 657) hydrogen bonds : angle 5.38368 ( 1731) SS BOND : bond 0.00289 ( 21) SS BOND : angle 2.29975 ( 42) covalent geometry : bond 0.00281 (17826) covalent geometry : angle 0.64010 (24180) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13394.56 seconds wall clock time: 236 minutes 50.64 seconds (14210.64 seconds total)