Starting phenix.real_space_refine on Thu Aug 6 18:41:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rge_53949/08_2026/9rge_53949.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rge_53949/08_2026/9rge_53949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rge_53949/08_2026/9rge_53949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rge_53949/08_2026/9rge_53949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rge_53949/08_2026/9rge_53949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rge_53949/08_2026/9rge_53949.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 99 5.16 5 C 10637 2.51 5 N 2573 2.21 5 O 2965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16281 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2788 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 330} Chain breaks: 1 Chain: "B" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2752 Classifications: {'peptide': 335} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2833 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 331} Chain breaks: 3 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2822 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 333} Chain breaks: 1 Chain: "E" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 332, 2728 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 332, 2728 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 bond proxies already assigned to first conformer: 2787 Chain: "H" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 214 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1421 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 179} Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {'HEX': 3, 'PIO': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'HEX': 1, 'PGW': 1, 'R16': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {'D10': 1, 'HEX': 1, 'PIO': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.33, per 1000 atoms: 0.20 Number of scatterers: 16281 At special positions: 0 Unit cell: (92.583, 110.079, 143.613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 P 7 15.00 O 2965 8.00 N 2573 7.00 C 10637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 128 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 5 " - " MAN F 6 " " MAN F 8 " - " MAN F 9 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 7 " - " MAN F 8 " " BMA G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " " BMA K 3 " - " MAN K 6 " " MAN K 4 " - " MAN K 5 " ALPHA1-6 " BMA F 3 " - " MAN F 7 " " MAN F 7 " - " MAN F 10 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG F 1 " - " ASN A 111 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 755.1 milliseconds 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3646 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 42.8% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.861A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 223 through 244 removed outlier: 5.093A pdb=" N LEU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix removed outlier: 3.756A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 276 Processing helix chain 'A' and resid 284 through 311 Processing helix chain 'A' and resid 390 through 416 Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.809A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 420 through 447 removed outlier: 3.675A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.529A pdb=" N TRP C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.695A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 294 through 323 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 397 through 400 removed outlier: 4.454A pdb=" N ALA C 400 " --> pdb=" O ILE C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 400' Processing helix chain 'C' and resid 401 through 427 removed outlier: 3.800A pdb=" N ILE C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix Processing helix chain 'D' and resid 13 through 23 removed outlier: 4.553A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.656A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 276 Processing helix chain 'D' and resid 284 through 311 removed outlier: 3.567A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 415 removed outlier: 4.284A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 238 Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 313 removed outlier: 3.794A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Proline residue: E 311 - end of helix Processing helix chain 'E' and resid 422 through 447 Proline residue: E 432 - end of helix Processing helix chain 'H' and resid 672 through 696 Processing helix chain 'L' and resid 20 through 43 Processing helix chain 'L' and resid 89 through 113 Processing helix chain 'L' and resid 114 through 118 removed outlier: 3.588A pdb=" N PHE L 117 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 146 Processing helix chain 'L' and resid 152 through 159 Processing helix chain 'L' and resid 174 through 201 removed outlier: 3.667A pdb=" N ILE L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU L 185 " --> pdb=" O ILE L 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 removed outlier: 4.429A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 7.145A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.339A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.529A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.151A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.242A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.060A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ARG C 144 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA C 121 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.060A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 58 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 184 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N MET C 57 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N SER C 186 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VAL C 59 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N VAL C 188 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N SER C 61 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL C 190 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 13.975A pdb=" N GLY C 63 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.452A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.209A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 61 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.526A pdb=" N THR D 61 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.233A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.360A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.650A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.264A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.264A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'L' and resid 64 through 66 912 hydrogen bonds defined for protein. 2636 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: 2.08 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2396 1.31 - 1.44: 4942 1.44 - 1.57: 9167 1.57 - 1.70: 10 1.70 - 1.83: 164 Bond restraints: 16679 Sorted by residual: bond pdb=" C P1L C 504 " pdb=" O P1L C 504 " ideal model delta sigma weight residual 1.244 1.360 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C P1L C 502 " pdb=" O P1L C 502 " ideal model delta sigma weight residual 1.244 1.360 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C19 PGW B 501 " pdb=" O03 PGW B 501 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 PGW B 501 " pdb=" O01 PGW B 501 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1A PIO A3901 " pdb=" O2C PIO A3901 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 16674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 22231 2.77 - 5.54: 337 5.54 - 8.31: 34 8.31 - 11.08: 7 11.08 - 13.85: 5 Bond angle restraints: 22614 Sorted by residual: angle pdb=" O1 PIO D 504 " pdb=" P1 PIO D 504 " pdb=" O13 PIO D 504 " ideal model delta sigma weight residual 97.64 111.49 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CA VAL B 111 " pdb=" C VAL B 111 " pdb=" O VAL B 111 " ideal model delta sigma weight residual 121.67 117.03 4.64 1.02e+00 9.61e-01 2.07e+01 angle pdb=" O11 PGW B 501 " pdb=" P PGW B 501 " pdb=" O12 PGW B 501 " ideal model delta sigma weight residual 98.90 111.87 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" O1 PIO A3901 " pdb=" P1 PIO A3901 " pdb=" O13 PIO A3901 " ideal model delta sigma weight residual 97.64 110.13 -12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N VAL B 111 " pdb=" CA VAL B 111 " pdb=" CB VAL B 111 " ideal model delta sigma weight residual 112.52 106.72 5.80 1.40e+00 5.10e-01 1.72e+01 ... (remaining 22609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 10033 33.80 - 67.61: 143 67.61 - 101.41: 37 101.41 - 135.22: 27 135.22 - 169.02: 2 Dihedral angle restraints: 10242 sinusoidal: 4585 harmonic: 5657 Sorted by residual: dihedral pdb=" CB CYS L 112 " pdb=" SG CYS L 112 " pdb=" SG CYS L 128 " pdb=" CB CYS L 128 " ideal model delta sinusoidal sigma weight residual 93.00 147.61 -54.61 1 1.00e+01 1.00e-02 4.04e+01 dihedral pdb=" C03 PGW B 501 " pdb=" C01 PGW B 501 " pdb=" C02 PGW B 501 " pdb=" O03 PGW B 501 " ideal model delta sinusoidal sigma weight residual -64.65 104.37 -169.02 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O01 PGW B 501 " pdb=" C01 PGW B 501 " pdb=" C02 PGW B 501 " pdb=" O03 PGW B 501 " ideal model delta sinusoidal sigma weight residual 59.30 -133.90 -166.80 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 10239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 2632 0.292 - 0.585: 6 0.585 - 0.877: 1 0.877 - 1.169: 0 1.169 - 1.461: 1 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 MAN F 8 " pdb=" O3 MAN F 7 " pdb=" C2 MAN F 8 " pdb=" O5 MAN F 8 " both_signs ideal model delta sigma weight residual False 2.40 0.94 1.46 2.00e-02 2.50e+03 5.34e+03 chirality pdb=" C1 MAN G 4 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.60 0.80 2.00e-02 2.50e+03 1.59e+03 chirality pdb=" C1 MAN F 6 " pdb=" O2 MAN F 5 " pdb=" C2 MAN F 6 " pdb=" O5 MAN F 6 " both_signs ideal model delta sigma weight residual False 2.40 1.88 0.52 2.00e-02 2.50e+03 6.63e+02 ... (remaining 2637 not shown) Planarity restraints: 2708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.202 2.00e-02 2.50e+03 1.72e-01 3.71e+02 pdb=" C7 NAG J 1 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.035 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.285 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.190 2.00e-02 2.50e+03 1.62e-01 3.28e+02 pdb=" C7 NAG M 1 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.267 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.155 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" C7 NAG K 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.207 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 2705 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 169 2.63 - 3.19: 14347 3.19 - 3.76: 24848 3.76 - 4.33: 35470 4.33 - 4.90: 59924 Nonbonded interactions: 134758 Sorted by model distance: nonbonded pdb=" O THR C 278 " pdb=" OG1 THR C 281 " model vdw 2.058 3.040 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.136 3.040 nonbonded pdb=" OG SER L 50 " pdb=" O ASP L 170 " model vdw 2.149 3.040 nonbonded pdb=" OG SER C 291 " pdb=" O14 PGW B 501 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR A 267 " pdb=" OH TYR A 294 " model vdw 2.191 3.040 ... (remaining 134753 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 416 or resid 3903)) selection = (chain 'D' and (resid 12 through 323 or resid 384 through 416 or resid 503)) } ncs_group { reference = (chain 'B' and (resid 9 through 313 or resid 421 through 442 or resid 444 throug \ h 447)) selection = (chain 'E' and (resid 9 through 442 or resid 444 through 447)) } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'M' } 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=0.46 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.006 0.116 16716 Z= 0.300 Angle : 0.905 19.946 22705 Z= 0.390 Chirality : 0.060 1.461 2640 Planarity : 0.007 0.172 2707 Dihedral : 14.885 169.025 6572 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1893 helix: 2.39 (0.19), residues: 714 sheet: -0.31 (0.23), residues: 426 loop : -0.68 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.020 0.001 TYR C 314 PHE 0.017 0.001 PHE D 304 TRP 0.009 0.001 TRP L 175 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (16679) covalent geometry : angle 0.79382 / 0.36 (22614) SS BOND : bond 0.00318 / 0.18 ( 8) SS BOND : angle 1.60265 / 0.88 ( 16) hydrogen bonds : bond 0.09519 / 6.19 ( 827) hydrogen bonds : angle 4.79410 / 3.36 ( 2636) Misc. bond : bond 0.10008 / 4.73 ( 4) link_ALPHA1-2 : bond 0.04673 / 2.18 ( 3) link_ALPHA1-2 : angle 5.13544 / 3.07 ( 9) link_ALPHA1-3 : bond 0.04604 / 2.59 ( 6) link_ALPHA1-3 : angle 6.51295 / 4.21 ( 18) link_ALPHA1-6 : bond 0.03558 / 1.96 ( 5) link_ALPHA1-6 : angle 6.37100 / 3.88 ( 15) link_BETA1-4 : bond 0.04610 / 2.77 ( 10) link_BETA1-4 : angle 9.12263 / 6.62 ( 30) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 8.11628 / 4.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8111 (p0) cc_final: 0.7869 (p0) REVERT: A 279 LYS cc_start: 0.8791 (mptt) cc_final: 0.8483 (mmtm) REVERT: B 155 GLU cc_start: 0.7918 (tt0) cc_final: 0.7503 (tt0) REVERT: B 207 ARG cc_start: 0.8778 (ttm170) cc_final: 0.8523 (tpp80) REVERT: B 312 GLN cc_start: 0.7376 (mm110) cc_final: 0.6863 (tp40) REVERT: C 120 ASP cc_start: 0.8300 (t70) cc_final: 0.8066 (t70) REVERT: C 409 PHE cc_start: 0.8182 (t80) cc_final: 0.7945 (t80) REVERT: D 58 MET cc_start: 0.8454 (mmm) cc_final: 0.7781 (mmm) REVERT: D 81 MET cc_start: 0.6987 (mmt) cc_final: 0.6494 (tpt) REVERT: D 123 GLU cc_start: 0.7883 (tt0) cc_final: 0.7534 (mt-10) REVERT: D 274 ARG cc_start: 0.8080 (tpt170) cc_final: 0.7843 (tpt170) REVERT: D 286 MET cc_start: 0.8642 (ttp) cc_final: 0.8385 (ttp) REVERT: E 268 LEU cc_start: 0.8501 (tt) cc_final: 0.8153 (mm) REVERT: E 426 TRP cc_start: 0.8250 (m100) cc_final: 0.7595 (m100) REVERT: L 166 TYR cc_start: 0.6352 (m-80) cc_final: 0.5950 (t80) REVERT: L 199 ASN cc_start: 0.6203 (m-40) cc_final: 0.5952 (m-40) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1208 time to fit residues: 47.4594 Evaluate side-chains 169 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 ASN D 111 ASN D 408 ASN E 148 GLN E 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077380 restraints weight = 39153.654| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.75 r_work: 0.2893 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16716 Z= 0.132 Angle : 0.609 10.252 22705 Z= 0.292 Chirality : 0.043 0.265 2640 Planarity : 0.004 0.050 2707 Dihedral : 13.367 178.630 3018 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.11 % Allowed : 7.31 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1893 helix: 2.39 (0.19), residues: 717 sheet: -0.14 (0.24), residues: 411 loop : -0.62 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 180 TYR 0.019 0.001 TYR B 299 PHE 0.017 0.001 PHE D 304 TRP 0.013 0.001 TRP L 175 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16679) covalent geometry : angle 0.57795 / 0.28 (22614) SS BOND : bond 0.00907 / 0.45 ( 8) SS BOND : angle 2.74031 / 1.61 ( 16) hydrogen bonds : bond 0.03991 / 2.67 ( 827) hydrogen bonds : angle 4.19488 / 2.95 ( 2636) Misc. bond : bond 0.00074 / 0.03 ( 4) link_ALPHA1-2 : bond 0.00785 / 0.38 ( 3) link_ALPHA1-2 : angle 1.28090 / 0.63 ( 9) link_ALPHA1-3 : bond 0.01418 / 0.71 ( 6) link_ALPHA1-3 : angle 3.00668 / 2.04 ( 18) link_ALPHA1-6 : bond 0.00637 / 0.34 ( 5) link_ALPHA1-6 : angle 2.75144 / 1.57 ( 15) link_BETA1-4 : bond 0.00390 / 0.21 ( 10) link_BETA1-4 : angle 3.60358 / 2.70 ( 30) link_NAG-ASN : bond 0.00034 / 0.02 ( 1) link_NAG-ASN : angle 4.29383 / 2.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8369 (p0) cc_final: 0.8124 (p0) REVERT: B 155 GLU cc_start: 0.7937 (tt0) cc_final: 0.7630 (tt0) REVERT: B 312 GLN cc_start: 0.7516 (mm110) cc_final: 0.6910 (tp40) REVERT: C 120 ASP cc_start: 0.7935 (t70) cc_final: 0.7668 (t0) REVERT: D 58 MET cc_start: 0.8451 (mmm) cc_final: 0.7787 (mmm) REVERT: D 81 MET cc_start: 0.6770 (mmt) cc_final: 0.6304 (tpt) REVERT: D 114 MET cc_start: 0.7956 (ppp) cc_final: 0.7705 (ppp) REVERT: D 286 MET cc_start: 0.8510 (ttp) cc_final: 0.8262 (ttp) REVERT: E 301 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8044 (t80) REVERT: E 426 TRP cc_start: 0.8153 (m100) cc_final: 0.7464 (m100) REVERT: H 676 LEU cc_start: 0.5965 (tp) cc_final: 0.5659 (mm) REVERT: H 679 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8079 (p) outliers start: 19 outliers final: 9 residues processed: 196 average time/residue: 0.1213 time to fit residues: 36.7009 Evaluate side-chains 178 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 301 PHE Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 77 CYS Chi-restraints excluded: chain L residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 103 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 ASN B 243 ASN D 204 GLN ** L 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.075966 restraints weight = 30496.533| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.27 r_work: 0.2881 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16716 Z= 0.226 Angle : 0.658 9.708 22705 Z= 0.323 Chirality : 0.046 0.326 2640 Planarity : 0.005 0.051 2707 Dihedral : 12.061 174.167 3018 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.58 % Allowed : 8.72 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1893 helix: 2.06 (0.19), residues: 716 sheet: -0.13 (0.24), residues: 414 loop : -0.68 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.020 0.002 TYR C 314 PHE 0.022 0.002 PHE D 304 TRP 0.013 0.001 TRP L 175 HIS 0.005 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (16679) covalent geometry : angle 0.63116 / 0.32 (22614) SS BOND : bond 0.00561 / 0.29 ( 8) SS BOND : angle 2.89267 / 1.86 ( 16) hydrogen bonds : bond 0.04699 / 3.19 ( 827) hydrogen bonds : angle 4.38341 / 3.07 ( 2636) Misc. bond : bond 0.00051 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00888 / 0.43 ( 3) link_ALPHA1-2 : angle 1.46121 / 0.74 ( 9) link_ALPHA1-3 : bond 0.01588 / 0.86 ( 6) link_ALPHA1-3 : angle 2.90198 / 1.97 ( 18) link_ALPHA1-6 : bond 0.00427 / 0.25 ( 5) link_ALPHA1-6 : angle 2.66200 / 1.53 ( 15) link_BETA1-4 : bond 0.00365 / 0.18 ( 10) link_BETA1-4 : angle 3.42542 / 2.60 ( 30) link_NAG-ASN : bond 0.00338 / 0.18 ( 1) link_NAG-ASN : angle 4.44968 / 2.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8723 (p0) cc_final: 0.8363 (p0) REVERT: A 279 LYS cc_start: 0.8889 (mptt) cc_final: 0.8573 (mmtm) REVERT: B 155 GLU cc_start: 0.8309 (tt0) cc_final: 0.7878 (tt0) REVERT: B 312 GLN cc_start: 0.7669 (mm110) cc_final: 0.6952 (tp40) REVERT: D 58 MET cc_start: 0.8602 (mmm) cc_final: 0.7944 (mmm) REVERT: D 81 MET cc_start: 0.6834 (mmt) cc_final: 0.6444 (tpt) REVERT: D 141 MET cc_start: 0.8471 (mtp) cc_final: 0.8206 (mtp) REVERT: E 182 GLU cc_start: 0.8033 (tt0) cc_final: 0.7764 (pt0) REVERT: E 268 LEU cc_start: 0.8641 (tp) cc_final: 0.8403 (mp) REVERT: E 283 MET cc_start: 0.8942 (mmm) cc_final: 0.8656 (mmm) REVERT: E 426 TRP cc_start: 0.8307 (m100) cc_final: 0.7638 (m100) REVERT: H 686 LEU cc_start: 0.7206 (tt) cc_final: 0.6968 (tt) outliers start: 27 outliers final: 15 residues processed: 195 average time/residue: 0.1294 time to fit residues: 38.3540 Evaluate side-chains 173 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain H residue 673 SER Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 77 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 41 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 418 ASN D 204 GLN E 90 GLN E 267 HIS H 690 ASN L 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075891 restraints weight = 30995.697| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.34 r_work: 0.2879 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16716 Z= 0.201 Angle : 0.625 9.697 22705 Z= 0.306 Chirality : 0.044 0.291 2640 Planarity : 0.004 0.059 2707 Dihedral : 11.487 172.358 3018 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.28 % Allowed : 9.19 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1893 helix: 2.05 (0.19), residues: 716 sheet: -0.15 (0.24), residues: 413 loop : -0.68 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 221 TYR 0.020 0.002 TYR B 299 PHE 0.021 0.002 PHE D 304 TRP 0.021 0.001 TRP L 175 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (16679) covalent geometry : angle 0.60191 / 0.30 (22614) SS BOND : bond 0.00644 / 0.29 ( 8) SS BOND : angle 2.00214 / 1.32 ( 16) hydrogen bonds : bond 0.04378 / 2.94 ( 827) hydrogen bonds : angle 4.32516 / 3.03 ( 2636) Misc. bond : bond 0.00046 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00871 / 0.42 ( 3) link_ALPHA1-2 : angle 1.46657 / 0.73 ( 9) link_ALPHA1-3 : bond 0.01579 / 0.88 ( 6) link_ALPHA1-3 : angle 2.87433 / 1.94 ( 18) link_ALPHA1-6 : bond 0.00626 / 0.35 ( 5) link_ALPHA1-6 : angle 2.62245 / 1.49 ( 15) link_BETA1-4 : bond 0.00289 / 0.15 ( 10) link_BETA1-4 : angle 3.09625 / 2.35 ( 30) link_NAG-ASN : bond 0.00266 / 0.14 ( 1) link_NAG-ASN : angle 4.34538 / 2.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8765 (p0) cc_final: 0.8367 (p0) REVERT: A 81 MET cc_start: 0.8467 (pmm) cc_final: 0.8103 (pmm) REVERT: A 279 LYS cc_start: 0.8903 (mptt) cc_final: 0.8553 (mmtm) REVERT: B 155 GLU cc_start: 0.8306 (tt0) cc_final: 0.7861 (tt0) REVERT: B 312 GLN cc_start: 0.7738 (mm110) cc_final: 0.7008 (tp40) REVERT: C 85 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8249 (mtp-110) REVERT: D 58 MET cc_start: 0.8623 (mmm) cc_final: 0.7924 (mmm) REVERT: D 81 MET cc_start: 0.6829 (mmt) cc_final: 0.6416 (tpt) REVERT: D 317 TRP cc_start: 0.8226 (t60) cc_final: 0.7759 (t60) REVERT: E 268 LEU cc_start: 0.8698 (tp) cc_final: 0.8355 (mp) REVERT: E 301 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8245 (t80) REVERT: E 426 TRP cc_start: 0.8295 (m100) cc_final: 0.7604 (m100) REVERT: H 672 TYR cc_start: 0.5762 (m-80) cc_final: 0.5524 (m-80) REVERT: L 112 CYS cc_start: 0.6953 (t) cc_final: 0.6690 (t) REVERT: L 153 GLU cc_start: 0.6871 (pm20) cc_final: 0.6656 (pm20) outliers start: 39 outliers final: 20 residues processed: 191 average time/residue: 0.1316 time to fit residues: 38.2411 Evaluate side-chains 181 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 301 PHE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain H residue 673 SER Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 77 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 28 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 242 GLN E 90 GLN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.076532 restraints weight = 33558.354| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.45 r_work: 0.2890 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16716 Z= 0.152 Angle : 0.587 10.055 22705 Z= 0.286 Chirality : 0.042 0.288 2640 Planarity : 0.004 0.051 2707 Dihedral : 10.787 171.906 3018 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.81 % Allowed : 10.01 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1893 helix: 2.13 (0.19), residues: 717 sheet: -0.07 (0.24), residues: 413 loop : -0.63 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 136 TYR 0.020 0.001 TYR B 299 PHE 0.018 0.001 PHE D 304 TRP 0.018 0.001 TRP L 175 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16679) covalent geometry : angle 0.56641 / 0.28 (22614) SS BOND : bond 0.00719 / 0.47 ( 8) SS BOND : angle 1.57519 / 1.01 ( 16) hydrogen bonds : bond 0.03973 / 2.67 ( 827) hydrogen bonds : angle 4.21348 / 2.95 ( 2636) Misc. bond : bond 0.00038 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00888 / 0.43 ( 3) link_ALPHA1-2 : angle 1.46167 / 0.73 ( 9) link_ALPHA1-3 : bond 0.01642 / 0.91 ( 6) link_ALPHA1-3 : angle 2.82084 / 1.91 ( 18) link_ALPHA1-6 : bond 0.00884 / 0.46 ( 5) link_ALPHA1-6 : angle 2.37229 / 1.35 ( 15) link_BETA1-4 : bond 0.00272 / 0.15 ( 10) link_BETA1-4 : angle 2.78335 / 2.10 ( 30) link_NAG-ASN : bond 0.00125 / 0.07 ( 1) link_NAG-ASN : angle 4.03008 / 2.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8754 (p0) cc_final: 0.8373 (p0) REVERT: A 81 MET cc_start: 0.8514 (pmm) cc_final: 0.8195 (pmm) REVERT: B 14 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8290 (mp0) REVERT: B 155 GLU cc_start: 0.8348 (tt0) cc_final: 0.7911 (tt0) REVERT: B 312 GLN cc_start: 0.7735 (mm110) cc_final: 0.6991 (tp40) REVERT: D 58 MET cc_start: 0.8651 (mmm) cc_final: 0.7969 (mmm) REVERT: D 81 MET cc_start: 0.6765 (mmt) cc_final: 0.6342 (tpt) REVERT: D 317 TRP cc_start: 0.8214 (t60) cc_final: 0.7741 (t60) REVERT: E 224 GLN cc_start: 0.9040 (tp40) cc_final: 0.8784 (tp-100) REVERT: E 268 LEU cc_start: 0.8663 (tp) cc_final: 0.8331 (mp) REVERT: E 283 MET cc_start: 0.8890 (mmm) cc_final: 0.8640 (mmm) REVERT: E 301 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (t80) REVERT: E 426 TRP cc_start: 0.8291 (m100) cc_final: 0.7845 (m100) REVERT: H 672 TYR cc_start: 0.5785 (m-80) cc_final: 0.5522 (m-80) outliers start: 31 outliers final: 18 residues processed: 199 average time/residue: 0.1280 time to fit residues: 38.5798 Evaluate side-chains 188 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 301 PHE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 77 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 8 optimal weight: 0.0270 chunk 140 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 ASN E 149 ASN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077780 restraints weight = 31500.313| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.37 r_work: 0.2915 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16716 Z= 0.124 Angle : 0.570 9.783 22705 Z= 0.278 Chirality : 0.041 0.286 2640 Planarity : 0.004 0.052 2707 Dihedral : 10.205 170.401 3018 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.58 % Allowed : 11.41 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1893 helix: 2.25 (0.19), residues: 718 sheet: -0.01 (0.25), residues: 413 loop : -0.55 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 180 TYR 0.020 0.001 TYR B 299 PHE 0.016 0.001 PHE D 304 TRP 0.016 0.001 TRP L 175 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16679) covalent geometry : angle 0.54883 / 0.27 (22614) SS BOND : bond 0.00562 / 0.37 ( 8) SS BOND : angle 2.47526 / 1.52 ( 16) hydrogen bonds : bond 0.03666 / 2.48 ( 827) hydrogen bonds : angle 4.12015 / 2.88 ( 2636) Misc. bond : bond 0.00026 / 0.01 ( 4) link_ALPHA1-2 : bond 0.00935 / 0.45 ( 3) link_ALPHA1-2 : angle 1.47213 / 0.73 ( 9) link_ALPHA1-3 : bond 0.01666 / 0.92 ( 6) link_ALPHA1-3 : angle 2.80006 / 1.89 ( 18) link_ALPHA1-6 : bond 0.01065 / 0.55 ( 5) link_ALPHA1-6 : angle 2.14926 / 1.23 ( 15) link_BETA1-4 : bond 0.00278 / 0.16 ( 10) link_BETA1-4 : angle 2.56382 / 1.92 ( 30) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 3.76798 / 2.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8696 (p0) cc_final: 0.8321 (p0) REVERT: A 81 MET cc_start: 0.8487 (pmm) cc_final: 0.8201 (pmm) REVERT: A 279 LYS cc_start: 0.8871 (mptt) cc_final: 0.8665 (mmtm) REVERT: B 14 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8271 (mp0) REVERT: B 155 GLU cc_start: 0.8334 (tt0) cc_final: 0.7898 (tt0) REVERT: B 270 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: B 312 GLN cc_start: 0.7709 (mm110) cc_final: 0.6974 (tp40) REVERT: D 58 MET cc_start: 0.8607 (mmm) cc_final: 0.7892 (mmm) REVERT: D 81 MET cc_start: 0.6753 (mmt) cc_final: 0.6427 (tpt) REVERT: D 317 TRP cc_start: 0.8176 (t60) cc_final: 0.7720 (t60) REVERT: E 224 GLN cc_start: 0.9018 (tp40) cc_final: 0.8793 (tp-100) REVERT: E 268 LEU cc_start: 0.8615 (tp) cc_final: 0.8366 (mp) REVERT: E 283 MET cc_start: 0.8872 (mmm) cc_final: 0.8540 (mmm) REVERT: E 301 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8213 (t80) REVERT: E 426 TRP cc_start: 0.8235 (m100) cc_final: 0.7778 (m100) REVERT: H 672 TYR cc_start: 0.5703 (m-80) cc_final: 0.5146 (m-80) REVERT: L 138 CYS cc_start: 0.8367 (t) cc_final: 0.8004 (t) REVERT: L 179 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7807 (mp) outliers start: 27 outliers final: 17 residues processed: 205 average time/residue: 0.1180 time to fit residues: 36.7955 Evaluate side-chains 193 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 301 PHE Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 77 CYS Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 ASN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078952 restraints weight = 29546.341| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.28 r_work: 0.2934 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16716 Z= 0.116 Angle : 0.550 10.230 22705 Z= 0.268 Chirality : 0.041 0.286 2640 Planarity : 0.004 0.052 2707 Dihedral : 9.741 165.232 3018 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.46 % Allowed : 11.76 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1893 helix: 2.30 (0.19), residues: 718 sheet: 0.13 (0.25), residues: 418 loop : -0.48 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 180 TYR 0.019 0.001 TYR B 299 PHE 0.016 0.001 PHE D 304 TRP 0.015 0.001 TRP L 175 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16679) covalent geometry : angle 0.53056 / 0.26 (22614) SS BOND : bond 0.00457 / 0.24 ( 8) SS BOND : angle 2.12806 / 1.33 ( 16) hydrogen bonds : bond 0.03477 / 2.35 ( 827) hydrogen bonds : angle 4.04210 / 2.83 ( 2636) Misc. bond : bond 0.00026 / 0.01 ( 4) link_ALPHA1-2 : bond 0.00896 / 0.43 ( 3) link_ALPHA1-2 : angle 1.44724 / 0.73 ( 9) link_ALPHA1-3 : bond 0.01697 / 0.92 ( 6) link_ALPHA1-3 : angle 2.82225 / 1.88 ( 18) link_ALPHA1-6 : bond 0.01008 / 0.53 ( 5) link_ALPHA1-6 : angle 1.76090 / 1.04 ( 15) link_BETA1-4 : bond 0.00279 / 0.16 ( 10) link_BETA1-4 : angle 2.43124 / 1.83 ( 30) link_NAG-ASN : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : angle 3.50193 / 1.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8650 (p0) cc_final: 0.8277 (p0) REVERT: A 81 MET cc_start: 0.8511 (pmm) cc_final: 0.8246 (pmm) REVERT: B 14 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8271 (mp0) REVERT: B 155 GLU cc_start: 0.8296 (tt0) cc_final: 0.7866 (tt0) REVERT: B 270 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: B 312 GLN cc_start: 0.7686 (mm110) cc_final: 0.6964 (tp40) REVERT: D 58 MET cc_start: 0.8570 (mmm) cc_final: 0.7897 (mmm) REVERT: D 81 MET cc_start: 0.6780 (mmt) cc_final: 0.6379 (tpt) REVERT: D 317 TRP cc_start: 0.8126 (t60) cc_final: 0.7682 (t60) REVERT: E 268 LEU cc_start: 0.8645 (tp) cc_final: 0.8368 (mp) REVERT: E 283 MET cc_start: 0.8863 (mmm) cc_final: 0.8532 (mmm) REVERT: E 301 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8202 (t80) REVERT: E 426 TRP cc_start: 0.8230 (m100) cc_final: 0.7764 (m100) REVERT: H 672 TYR cc_start: 0.5677 (m-80) cc_final: 0.5146 (m-80) REVERT: L 175 TRP cc_start: 0.7376 (p-90) cc_final: 0.7025 (p-90) outliers start: 25 outliers final: 17 residues processed: 198 average time/residue: 0.1246 time to fit residues: 37.1987 Evaluate side-chains 190 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 301 PHE Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 77 CYS Chi-restraints excluded: chain L residue 112 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 126 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 ASN C 60 ASN D 242 GLN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.074181 restraints weight = 33254.863| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.42 r_work: 0.2846 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16716 Z= 0.288 Angle : 0.683 11.658 22705 Z= 0.336 Chirality : 0.046 0.326 2640 Planarity : 0.005 0.058 2707 Dihedral : 10.441 155.139 3018 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.05 % Allowed : 11.94 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1893 helix: 1.91 (0.19), residues: 716 sheet: 0.00 (0.25), residues: 417 loop : -0.65 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 180 TYR 0.023 0.002 TYR C 314 PHE 0.026 0.002 PHE D 304 TRP 0.015 0.002 TRP L 26 HIS 0.007 0.002 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.29 (16679) covalent geometry : angle 0.66305 / 0.33 (22614) SS BOND : bond 0.00632 / 0.28 ( 8) SS BOND : angle 2.34075 / 1.47 ( 16) hydrogen bonds : bond 0.04864 / 3.28 ( 827) hydrogen bonds : angle 4.41716 / 3.10 ( 2636) Misc. bond : bond 0.00074 / 0.04 ( 4) link_ALPHA1-2 : bond 0.00841 / 0.41 ( 3) link_ALPHA1-2 : angle 1.61151 / 0.83 ( 9) link_ALPHA1-3 : bond 0.01612 / 0.88 ( 6) link_ALPHA1-3 : angle 2.92093 / 1.93 ( 18) link_ALPHA1-6 : bond 0.00642 / 0.33 ( 5) link_ALPHA1-6 : angle 2.23848 / 1.27 ( 15) link_BETA1-4 : bond 0.00323 / 0.16 ( 10) link_BETA1-4 : angle 2.84359 / 2.15 ( 30) link_NAG-ASN : bond 0.00526 / 0.28 ( 1) link_NAG-ASN : angle 4.66503 / 2.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8825 (p0) cc_final: 0.8443 (p0) REVERT: A 81 MET cc_start: 0.8530 (pmm) cc_final: 0.8230 (pmm) REVERT: B 14 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8300 (mp0) REVERT: B 155 GLU cc_start: 0.8336 (tt0) cc_final: 0.7886 (tt0) REVERT: B 270 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: B 312 GLN cc_start: 0.7733 (mm110) cc_final: 0.6975 (tp-100) REVERT: D 58 MET cc_start: 0.8606 (mmm) cc_final: 0.7881 (mmm) REVERT: D 81 MET cc_start: 0.6888 (mmt) cc_final: 0.6631 (tpt) REVERT: D 141 MET cc_start: 0.8527 (mtp) cc_final: 0.8273 (mtp) REVERT: D 317 TRP cc_start: 0.8195 (t60) cc_final: 0.7803 (t60) REVERT: E 268 LEU cc_start: 0.8725 (tp) cc_final: 0.8386 (mp) REVERT: E 426 TRP cc_start: 0.8326 (m100) cc_final: 0.7878 (m100) outliers start: 35 outliers final: 25 residues processed: 184 average time/residue: 0.1183 time to fit residues: 33.0181 Evaluate side-chains 189 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 77 CYS Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain L residue 139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 90 GLN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077107 restraints weight = 38529.632| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.64 r_work: 0.2893 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16716 Z= 0.115 Angle : 0.563 10.546 22705 Z= 0.275 Chirality : 0.041 0.288 2640 Planarity : 0.004 0.051 2707 Dihedral : 9.772 151.449 3018 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.11 % Allowed : 12.99 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1893 helix: 2.21 (0.19), residues: 717 sheet: 0.13 (0.25), residues: 405 loop : -0.57 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 180 TYR 0.021 0.001 TYR B 299 PHE 0.014 0.001 PHE A 304 TRP 0.025 0.001 TRP L 175 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16679) covalent geometry : angle 0.54541 / 0.27 (22614) SS BOND : bond 0.00407 / 0.19 ( 8) SS BOND : angle 1.94399 / 1.18 ( 16) hydrogen bonds : bond 0.03640 / 2.46 ( 827) hydrogen bonds : angle 4.12535 / 2.89 ( 2636) Misc. bond : bond 0.00030 / 0.01 ( 4) link_ALPHA1-2 : bond 0.00915 / 0.44 ( 3) link_ALPHA1-2 : angle 1.59358 / 0.79 ( 9) link_ALPHA1-3 : bond 0.01654 / 0.90 ( 6) link_ALPHA1-3 : angle 2.74675 / 1.83 ( 18) link_ALPHA1-6 : bond 0.00863 / 0.46 ( 5) link_ALPHA1-6 : angle 1.70372 / 1.04 ( 15) link_BETA1-4 : bond 0.00292 / 0.17 ( 10) link_BETA1-4 : angle 2.38309 / 1.78 ( 30) link_NAG-ASN : bond 0.00081 / 0.04 ( 1) link_NAG-ASN : angle 3.68515 / 1.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8502 (p0) cc_final: 0.8140 (p0) REVERT: A 81 MET cc_start: 0.8482 (pmm) cc_final: 0.8180 (pmm) REVERT: B 14 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8130 (mp0) REVERT: B 155 GLU cc_start: 0.8040 (tt0) cc_final: 0.7587 (tt0) REVERT: B 270 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: B 312 GLN cc_start: 0.7613 (mm110) cc_final: 0.6904 (tp40) REVERT: D 58 MET cc_start: 0.8482 (mmm) cc_final: 0.7815 (mmm) REVERT: D 81 MET cc_start: 0.6898 (mmt) cc_final: 0.6501 (tpt) REVERT: D 317 TRP cc_start: 0.8042 (t60) cc_final: 0.7594 (t60) REVERT: E 218 ILE cc_start: 0.8973 (pp) cc_final: 0.8584 (mt) REVERT: E 268 LEU cc_start: 0.8624 (tp) cc_final: 0.8358 (mp) REVERT: E 426 TRP cc_start: 0.8140 (m100) cc_final: 0.7753 (m100) REVERT: H 670 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6947 (ttm-80) REVERT: L 153 GLU cc_start: 0.6716 (pm20) cc_final: 0.6509 (pm20) outliers start: 19 outliers final: 15 residues processed: 187 average time/residue: 0.1125 time to fit residues: 31.7068 Evaluate side-chains 190 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 77 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 ASN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076874 restraints weight = 40479.748| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.75 r_work: 0.2883 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16716 Z= 0.122 Angle : 0.561 11.970 22705 Z= 0.274 Chirality : 0.041 0.289 2640 Planarity : 0.004 0.052 2707 Dihedral : 9.435 134.677 3018 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.05 % Allowed : 12.81 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1893 helix: 2.27 (0.19), residues: 718 sheet: 0.21 (0.25), residues: 408 loop : -0.56 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 85 TYR 0.020 0.001 TYR B 299 PHE 0.017 0.001 PHE D 304 TRP 0.021 0.001 TRP L 175 HIS 0.009 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16679) covalent geometry : angle 0.54400 / 0.27 (22614) SS BOND : bond 0.00416 / 0.19 ( 8) SS BOND : angle 1.90611 / 1.15 ( 16) hydrogen bonds : bond 0.03624 / 2.45 ( 827) hydrogen bonds : angle 4.07778 / 2.85 ( 2636) Misc. bond : bond 0.00039 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00878 / 0.43 ( 3) link_ALPHA1-2 : angle 1.51523 / 0.76 ( 9) link_ALPHA1-3 : bond 0.01642 / 0.89 ( 6) link_ALPHA1-3 : angle 2.75692 / 1.84 ( 18) link_ALPHA1-6 : bond 0.00812 / 0.44 ( 5) link_ALPHA1-6 : angle 1.59079 / 0.95 ( 15) link_BETA1-4 : bond 0.00267 / 0.15 ( 10) link_BETA1-4 : angle 2.41332 / 1.81 ( 30) link_NAG-ASN : bond 0.00034 / 0.02 ( 1) link_NAG-ASN : angle 3.53579 / 1.95 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8507 (p0) cc_final: 0.8144 (p0) REVERT: A 81 MET cc_start: 0.8488 (pmm) cc_final: 0.8191 (pmm) REVERT: B 14 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8157 (mp0) REVERT: B 155 GLU cc_start: 0.8066 (tt0) cc_final: 0.7615 (tt0) REVERT: B 270 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: B 312 GLN cc_start: 0.7573 (mm110) cc_final: 0.6846 (tp40) REVERT: D 58 MET cc_start: 0.8459 (mmm) cc_final: 0.7767 (mmm) REVERT: D 81 MET cc_start: 0.6892 (mmt) cc_final: 0.6292 (tpt) REVERT: D 123 GLU cc_start: 0.8262 (pp20) cc_final: 0.7850 (mt-10) REVERT: D 317 TRP cc_start: 0.8058 (t60) cc_final: 0.7631 (t60) REVERT: E 218 ILE cc_start: 0.8956 (pp) cc_final: 0.8624 (mt) REVERT: E 268 LEU cc_start: 0.8617 (tp) cc_final: 0.8350 (mp) REVERT: E 426 TRP cc_start: 0.8142 (m100) cc_final: 0.7740 (m100) REVERT: H 670 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6948 (ttm-80) REVERT: L 153 GLU cc_start: 0.6730 (pm20) cc_final: 0.6518 (pm20) outliers start: 18 outliers final: 16 residues processed: 185 average time/residue: 0.1163 time to fit residues: 32.5069 Evaluate side-chains 191 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain H residue 679 THR Chi-restraints excluded: chain L residue 77 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 147 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.075951 restraints weight = 31696.114| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.43 r_work: 0.2883 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16716 Z= 0.170 Angle : 0.594 12.357 22705 Z= 0.291 Chirality : 0.043 0.305 2640 Planarity : 0.004 0.053 2707 Dihedral : 9.393 109.338 3018 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.40 % Allowed : 12.58 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1893 helix: 2.18 (0.19), residues: 718 sheet: 0.14 (0.25), residues: 406 loop : -0.59 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 85 TYR 0.020 0.001 TYR B 299 PHE 0.020 0.001 PHE D 304 TRP 0.020 0.001 TRP L 175 HIS 0.009 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (16679) covalent geometry : angle 0.57636 / 0.29 (22614) SS BOND : bond 0.00498 / 0.22 ( 8) SS BOND : angle 1.97728 / 1.18 ( 16) hydrogen bonds : bond 0.04017 / 2.71 ( 827) hydrogen bonds : angle 4.17400 / 2.92 ( 2636) Misc. bond : bond 0.00045 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00877 / 0.42 ( 3) link_ALPHA1-2 : angle 1.48369 / 0.75 ( 9) link_ALPHA1-3 : bond 0.01616 / 0.88 ( 6) link_ALPHA1-3 : angle 2.80183 / 1.86 ( 18) link_ALPHA1-6 : bond 0.00722 / 0.39 ( 5) link_ALPHA1-6 : angle 1.68067 / 0.99 ( 15) link_BETA1-4 : bond 0.00244 / 0.13 ( 10) link_BETA1-4 : angle 2.48676 / 1.88 ( 30) link_NAG-ASN : bond 0.00193 / 0.10 ( 1) link_NAG-ASN : angle 3.82051 / 2.11 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4224.90 seconds wall clock time: 72 minutes 59.48 seconds (4379.48 seconds total)