Starting phenix.real_space_refine on Fri Jul 3 11:57:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zb5_73975/07_2026/9zb5_73975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zb5_73975/07_2026/9zb5_73975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zb5_73975/07_2026/9zb5_73975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zb5_73975/07_2026/9zb5_73975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zb5_73975/07_2026/9zb5_73975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zb5_73975/07_2026/9zb5_73975.map" } resolution = 3.29 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= 0.004 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8626 2.51 5 N 2344 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13658 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 991 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 124} Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 991 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 124} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 808 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "F" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 405} Chain: "G" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 838 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 808 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "I" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 743 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 101} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "J" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 405} Chain: "M" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 838 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "N" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 743 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 101} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'FUC': 1, 'NAG': 3} 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: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'FUC': 1, 'NAG': 3} 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: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'FUC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'FUC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.81, per 1000 atoms: 0.21 Number of scatterers: 13658 At special positions: 0 Unit cell: (126.04, 117.272, 135.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2620 8.00 N 2344 7.00 C 8626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 460 " distance=2.03 Simple disulfide: pdb=" SG CYS F 79 " - pdb=" SG CYS F 103 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 239 " - pdb=" SG CYS F 252 " distance=2.03 Simple disulfide: pdb=" SG CYS F 244 " - pdb=" SG CYS F 358 " distance=2.03 Simple disulfide: pdb=" SG CYS F 352 " - pdb=" SG CYS F 362 " distance=2.03 Simple disulfide: pdb=" SG CYS F 424 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 431 " distance=2.03 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 116 " - pdb=" SG CYS J 129 " distance=2.03 Simple disulfide: pdb=" SG CYS J 210 " - pdb=" SG CYS J 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 329 " distance=2.03 Simple disulfide: pdb=" SG CYS J 323 " - pdb=" SG CYS J 333 " distance=2.03 Simple disulfide: pdb=" SG CYS J 395 " - pdb=" SG CYS J 404 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 93 " 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=0, symmetry=0 Links applied BETA1-4 " NAG K 2 " - " NAG K 3 " " NAG L 2 " - " NAG L 3 " BETA1-6 " NAG K 2 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG L 2 " - " FUC L 4 " NAG-ASN " NAG K 1 " - " ASN F 412 " " NAG L 1 " - " ASN J 383 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 594.9 milliseconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 40 sheets defined 3.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 248 through 254 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 219 through 225 Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.516A pdb=" N SER M 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.600A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.355A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.679A pdb=" N VAL C 46 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA6, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.596A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.475A pdb=" N THR D 127 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 12 " --> pdb=" O THR D 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.643A pdb=" N VAL D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AB1, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB2, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 49 removed outlier: 6.980A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA E 90 " --> pdb=" O ASP E 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 91 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 101 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 37 through 39 Processing sheet with id=AB5, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AB6, first strand: chain 'F' and resid 79 through 87 removed outlier: 6.798A pdb=" N THR F 95 " --> pdb=" O PRO F 83 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU F 85 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA F 93 " --> pdb=" O LEU F 85 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU F 113 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER F 133 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 115 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 149 removed outlier: 5.575A pdb=" N SER F 144 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER F 159 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 148 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP F 176 " --> pdb=" O THR F 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 208 through 209 Processing sheet with id=AB9, first strand: chain 'F' and resid 208 through 209 removed outlier: 3.853A pdb=" N ILE F 221 " --> pdb=" O ALA F 273 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 271 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG F 265 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 299 through 304 removed outlier: 3.557A pdb=" N LEU F 304 " --> pdb=" O LYS F 307 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS F 307 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE F 308 " --> pdb=" O ILE F 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 370 through 372 Processing sheet with id=AC3, first strand: chain 'F' and resid 440 through 441 removed outlier: 3.576A pdb=" N HIS F 441 " --> pdb=" O THR F 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.668A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.768A pdb=" N SER G 35 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 49 through 51 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AC8, first strand: chain 'H' and resid 47 through 49 removed outlier: 6.931A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 47 through 49 removed outlier: 6.931A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA H 90 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR H 91 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL H 101 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 19 through 23 Processing sheet with id=AD2, first strand: chain 'J' and resid 8 through 10 Processing sheet with id=AD3, first strand: chain 'J' and resid 23 through 26 Processing sheet with id=AD4, first strand: chain 'J' and resid 50 through 58 removed outlier: 6.596A pdb=" N THR J 66 " --> pdb=" O PRO J 54 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU J 56 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA J 64 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER J 67 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU J 84 " --> pdb=" O SER J 104 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER J 104 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE J 86 " --> pdb=" O ARG J 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 114 through 120 removed outlier: 5.630A pdb=" N SER J 115 " --> pdb=" O SER J 130 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER J 130 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA J 119 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP J 147 " --> pdb=" O THR J 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 150 " --> pdb=" O THR J 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 179 through 180 Processing sheet with id=AD7, first strand: chain 'J' and resid 179 through 180 removed outlier: 3.848A pdb=" N ILE J 192 " --> pdb=" O ALA J 244 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 242 " --> pdb=" O PHE J 194 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG J 236 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 270 through 275 removed outlier: 3.521A pdb=" N LEU J 275 " --> pdb=" O LYS J 278 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS J 278 " --> pdb=" O LEU J 275 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE J 279 " --> pdb=" O ILE J 297 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 341 through 343 Processing sheet with id=AE1, first strand: chain 'J' and resid 411 through 412 removed outlier: 3.506A pdb=" N HIS J 412 " --> pdb=" O THR J 417 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.625A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER M 7 " --> pdb=" O SER M 21 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER M 35 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU M 37 " --> pdb=" O TYR M 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 23 294 hydrogen bonds defined for protein. 717 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: 1.72 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4404 1.34 - 1.46: 3064 1.46 - 1.58: 6428 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 13988 Sorted by residual: bond pdb=" CA HIS D 35 " pdb=" CB HIS D 35 " ideal model delta sigma weight residual 1.526 1.566 -0.040 1.70e-02 3.46e+03 5.59e+00 bond pdb=" CA PHE M 106 " pdb=" CB PHE M 106 " ideal model delta sigma weight residual 1.525 1.551 -0.026 1.47e-02 4.63e+03 3.21e+00 bond pdb=" C6 NAG K 1 " pdb=" O6 NAG K 1 " ideal model delta sigma weight residual 1.408 1.442 -0.034 2.00e-02 2.50e+03 2.91e+00 bond pdb=" C6 NAG L 1 " pdb=" O6 NAG L 1 " ideal model delta sigma weight residual 1.408 1.442 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" CA PHE H 50 " pdb=" CB PHE H 50 " ideal model delta sigma weight residual 1.526 1.544 -0.018 1.44e-02 4.82e+03 1.56e+00 ... (remaining 13983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18249 1.93 - 3.85: 715 3.85 - 5.78: 101 5.78 - 7.71: 21 7.71 - 9.64: 6 Bond angle restraints: 19092 Sorted by residual: angle pdb=" C ASN H 97 " pdb=" CA ASN H 97 " pdb=" CB ASN H 97 " ideal model delta sigma weight residual 117.23 110.06 7.17 1.36e+00 5.41e-01 2.78e+01 angle pdb=" N THR J 300 " pdb=" CA THR J 300 " pdb=" C THR J 300 " ideal model delta sigma weight residual 112.72 106.26 6.46 1.28e+00 6.10e-01 2.54e+01 angle pdb=" C ASN E 97 " pdb=" CA ASN E 97 " pdb=" CB ASN E 97 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" N HIS G 56 " pdb=" CA HIS G 56 " pdb=" C HIS G 56 " ideal model delta sigma weight residual 114.75 108.81 5.94 1.26e+00 6.30e-01 2.22e+01 angle pdb=" N VAL H 3 " pdb=" CA VAL H 3 " pdb=" C VAL H 3 " ideal model delta sigma weight residual 112.80 107.39 5.41 1.15e+00 7.56e-01 2.22e+01 ... (remaining 19087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 7153 18.01 - 36.03: 902 36.03 - 54.04: 257 54.04 - 72.05: 54 72.05 - 90.07: 14 Dihedral angle restraints: 8380 sinusoidal: 3246 harmonic: 5134 Sorted by residual: dihedral pdb=" CA ASP C 118 " pdb=" C ASP C 118 " pdb=" N PRO C 119 " pdb=" CA PRO C 119 " ideal model delta harmonic sigma weight residual 180.00 117.50 62.50 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA ASP D 118 " pdb=" C ASP D 118 " pdb=" N PRO D 119 " pdb=" CA PRO D 119 " ideal model delta harmonic sigma weight residual 180.00 121.23 58.77 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CB CYS J 215 " pdb=" SG CYS J 215 " pdb=" SG CYS J 329 " pdb=" CB CYS J 329 " ideal model delta sinusoidal sigma weight residual 93.00 29.42 63.58 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 8377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1986 0.088 - 0.176: 180 0.176 - 0.264: 3 0.264 - 0.352: 1 0.352 - 0.441: 2 Chirality restraints: 2172 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN J 383 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN F 412 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C5 NAG L 2 " pdb=" C4 NAG L 2 " pdb=" C6 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.14 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2169 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 50 " 0.016 2.00e-02 2.50e+03 1.78e-02 5.55e+00 pdb=" CG PHE H 50 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE H 50 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE H 50 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE H 50 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 50 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 50 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 50 " -0.014 2.00e-02 2.50e+03 1.72e-02 5.20e+00 pdb=" CG PHE E 50 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 50 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE E 50 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 118 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 119 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.029 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 6 1.92 - 2.67: 222 2.67 - 3.41: 17118 3.41 - 4.16: 31052 4.16 - 4.90: 55645 Nonbonded interactions: 104043 Sorted by model distance: nonbonded pdb=" O6 NAG K 1 " pdb=" O5 NAG K 2 " model vdw 1.177 3.040 nonbonded pdb=" O6 NAG L 1 " pdb=" O5 NAG L 2 " model vdw 1.183 3.040 nonbonded pdb=" O6 NAG K 1 " pdb=" C5 NAG K 2 " model vdw 1.383 3.470 nonbonded pdb=" O6 NAG L 1 " pdb=" C5 NAG L 2 " model vdw 1.384 3.470 nonbonded pdb=" O6 NAG L 1 " pdb=" C6 NAG L 2 " model vdw 1.588 3.440 ... (remaining 104038 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 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.220 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.003 0.040 14016 Z= 0.182 Angle : 0.883 9.637 19154 Z= 0.519 Chirality : 0.048 0.441 2172 Planarity : 0.005 0.051 2450 Dihedral : 17.584 90.066 5050 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.78 % Favored : 86.66 % Rotamer: Outliers : 4.56 % Allowed : 29.81 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 3.92 % 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: -4.29 (0.18), residues: 1776 helix: -1.85 (0.96), residues: 28 sheet: -1.88 (0.20), residues: 645 loop : -3.71 (0.15), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 413 TYR 0.019 0.001 TYR I 91 PHE 0.041 0.002 PHE H 50 TRP 0.026 0.002 TRP I 40 HIS 0.003 0.001 HIS F 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (13988) covalent geometry : angle 0.87815 / 0.52 (19092) SS BOND : bond 0.00154 / 0.10 ( 22) SS BOND : angle 1.23038 / 0.82 ( 44) hydrogen bonds : bond 0.26389 / 17.51 ( 289) hydrogen bonds : angle 9.72695 / 6.69 ( 717) link_BETA1-4 : bond 0.00470 / 0.24 ( 2) link_BETA1-4 : angle 2.12759 / 1.19 ( 6) link_BETA1-6 : bond 0.00164 / 0.09 ( 2) link_BETA1-6 : angle 1.52948 / 0.74 ( 6) link_NAG-ASN : bond 0.00581 / 0.29 ( 2) link_NAG-ASN : angle 3.89060 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.6424 (mmm) cc_final: 0.5984 (mmm) REVERT: C 47 TRP cc_start: 0.6601 (t60) cc_final: 0.6399 (t60) REVERT: C 83 MET cc_start: 0.3825 (OUTLIER) cc_final: 0.0065 (mpt) REVERT: D 34 MET cc_start: 0.6598 (mmm) cc_final: 0.6244 (mmt) REVERT: D 120 TRP cc_start: 0.5940 (m100) cc_final: 0.5523 (m100) REVERT: E 46 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7275 (ttp80) REVERT: F 57 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.5913 (tptt) REVERT: F 62 ARG cc_start: 0.8355 (ptp-170) cc_final: 0.7682 (mtm110) REVERT: F 81 ARG cc_start: 0.8390 (mtm180) cc_final: 0.7670 (mmm160) REVERT: F 104 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7201 (tp-100) REVERT: F 166 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7526 (ttt180) REVERT: F 174 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7119 (pt) REVERT: F 184 TYR cc_start: 0.5999 (OUTLIER) cc_final: 0.4569 (t80) REVERT: F 270 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6557 (mp) REVERT: F 413 ARG cc_start: 0.8162 (mtt90) cc_final: 0.6884 (mtp180) REVERT: F 425 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7405 (pp) REVERT: G 78 THR cc_start: 0.8008 (p) cc_final: 0.7725 (p) REVERT: G 106 PHE cc_start: 0.6934 (m-80) cc_final: 0.6616 (m-80) REVERT: I 54 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.4272 (m-10) REVERT: J 9 LYS cc_start: 0.7659 (pttp) cc_final: 0.7204 (ptpp) REVERT: J 28 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.6245 (tptt) REVERT: J 52 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7525 (mmm160) REVERT: J 102 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7385 (ttm170) REVERT: J 137 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.7666 (ttt180) REVERT: J 155 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4838 (t80) REVERT: J 378 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8210 (mm-30) REVERT: J 384 ARG cc_start: 0.8090 (mtt90) cc_final: 0.6803 (mtp180) REVERT: M 78 THR cc_start: 0.8057 (p) cc_final: 0.7758 (p) REVERT: N 54 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5285 (m-80) outliers start: 66 outliers final: 52 residues processed: 221 average time/residue: 0.1337 time to fit residues: 42.0281 Evaluate side-chains 220 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 308 LYS Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.0770 chunk 149 optimal weight: 0.0770 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.212318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164559 restraints weight = 14858.632| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.51 r_work: 0.3591 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14016 Z= 0.110 Angle : 0.676 9.887 19154 Z= 0.336 Chirality : 0.049 0.602 2172 Planarity : 0.005 0.054 2450 Dihedral : 9.521 59.664 2261 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.77 % Favored : 87.73 % Rotamer: Outliers : 6.71 % Allowed : 26.69 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 3.92 % 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: -3.97 (0.18), residues: 1776 helix: -1.63 (0.93), residues: 31 sheet: -1.43 (0.20), residues: 666 loop : -3.69 (0.15), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 384 TYR 0.013 0.001 TYR I 91 PHE 0.020 0.001 PHE D 117 TRP 0.013 0.001 TRP I 40 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13988) covalent geometry : angle 0.66718 / 0.33 (19092) SS BOND : bond 0.00219 / 0.14 ( 22) SS BOND : angle 0.82049 / 0.52 ( 44) hydrogen bonds : bond 0.03864 / 2.54 ( 289) hydrogen bonds : angle 6.29367 / 4.34 ( 717) link_BETA1-4 : bond 0.01924 / 0.96 ( 2) link_BETA1-4 : angle 2.21342 / 1.20 ( 6) link_BETA1-6 : bond 0.00747 / 0.38 ( 2) link_BETA1-6 : angle 1.64226 / 0.82 ( 6) link_NAG-ASN : bond 0.00454 / 0.23 ( 2) link_NAG-ASN : angle 5.32274 / 2.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 176 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: C 34 MET cc_start: 0.6446 (mmm) cc_final: 0.6040 (mmm) REVERT: C 83 MET cc_start: 0.3546 (OUTLIER) cc_final: 0.0279 (mpt) REVERT: D 34 MET cc_start: 0.6503 (mmm) cc_final: 0.6295 (mmm) REVERT: D 97 VAL cc_start: 0.7396 (p) cc_final: 0.6498 (t) REVERT: F 57 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.5833 (tptt) REVERT: F 131 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7480 (mpt180) REVERT: F 184 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.4500 (t80) REVERT: F 413 ARG cc_start: 0.7941 (mtt90) cc_final: 0.6780 (mtp180) REVERT: G 19 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7834 (ttm170) REVERT: G 78 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7515 (p) REVERT: G 106 PHE cc_start: 0.6913 (m-80) cc_final: 0.6632 (m-80) REVERT: I 54 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.4097 (m-10) REVERT: J 28 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.6185 (tptt) REVERT: J 75 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7454 (mm-40) REVERT: J 102 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7540 (mpt180) REVERT: J 155 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.4308 (t80) REVERT: J 378 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8096 (mm-30) REVERT: J 384 ARG cc_start: 0.7916 (mtt90) cc_final: 0.6629 (mtp180) REVERT: J 414 SER cc_start: 0.8097 (t) cc_final: 0.7817 (t) REVERT: M 78 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7438 (p) REVERT: N 33 ASP cc_start: 0.6585 (t0) cc_final: 0.6334 (t0) REVERT: N 54 TYR cc_start: 0.5950 (OUTLIER) cc_final: 0.4446 (m-10) outliers start: 97 outliers final: 56 residues processed: 252 average time/residue: 0.1199 time to fit residues: 44.1452 Evaluate side-chains 227 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.205210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158066 restraints weight = 14994.142| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.70 r_work: 0.3496 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14016 Z= 0.190 Angle : 0.735 9.299 19154 Z= 0.373 Chirality : 0.051 0.524 2172 Planarity : 0.005 0.061 2450 Dihedral : 8.725 59.989 2214 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.53 % Favored : 84.97 % Rotamer: Outliers : 7.40 % Allowed : 26.35 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 3.92 % 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: -3.93 (0.18), residues: 1776 helix: -1.76 (0.89), residues: 30 sheet: -1.45 (0.20), residues: 684 loop : -3.65 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 72 TYR 0.023 0.002 TYR I 91 PHE 0.021 0.002 PHE D 117 TRP 0.020 0.002 TRP M 111 HIS 0.006 0.002 HIS J 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (13988) covalent geometry : angle 0.72652 / 0.37 (19092) SS BOND : bond 0.00363 / 0.21 ( 22) SS BOND : angle 1.21609 / 0.81 ( 44) hydrogen bonds : bond 0.04163 / 2.72 ( 289) hydrogen bonds : angle 5.80516 / 3.97 ( 717) link_BETA1-4 : bond 0.00064 / 0.03 ( 2) link_BETA1-4 : angle 2.51571 / 1.40 ( 6) link_BETA1-6 : bond 0.00357 / 0.18 ( 2) link_BETA1-6 : angle 1.77558 / 0.95 ( 6) link_NAG-ASN : bond 0.00496 / 0.25 ( 2) link_NAG-ASN : angle 5.01330 / 2.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 157 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.6295 (mmm) cc_final: 0.5780 (mmm) REVERT: C 120 TRP cc_start: 0.5540 (m100) cc_final: 0.5112 (m100) REVERT: C 122 GLN cc_start: 0.5471 (mp10) cc_final: 0.5169 (mp10) REVERT: D 34 MET cc_start: 0.6098 (mmm) cc_final: 0.5714 (mmm) REVERT: D 97 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7351 (p) REVERT: E 46 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6825 (ttp80) REVERT: F 57 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6264 (tptt) REVERT: F 104 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8176 (mm-40) REVERT: F 184 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.4657 (t80) REVERT: F 277 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.4394 (pp) REVERT: F 413 ARG cc_start: 0.8028 (mtt90) cc_final: 0.6940 (mtp180) REVERT: G 78 THR cc_start: 0.7964 (p) cc_final: 0.7616 (p) REVERT: I 54 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.4042 (m-10) REVERT: J 28 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.6417 (tptt) REVERT: J 155 TYR cc_start: 0.5860 (OUTLIER) cc_final: 0.4426 (t80) REVERT: J 248 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4461 (pp) REVERT: J 384 ARG cc_start: 0.8140 (mtt90) cc_final: 0.6943 (mtp180) REVERT: J 414 SER cc_start: 0.8191 (t) cc_final: 0.7866 (t) REVERT: N 54 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.4324 (m-10) outliers start: 107 outliers final: 80 residues processed: 245 average time/residue: 0.1085 time to fit residues: 39.9299 Evaluate side-chains 244 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 155 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 310 THR Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 92 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 159 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.208245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160012 restraints weight = 14908.614| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.37 r_work: 0.3564 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14016 Z= 0.118 Angle : 0.650 8.035 19154 Z= 0.327 Chirality : 0.048 0.476 2172 Planarity : 0.005 0.061 2450 Dihedral : 8.349 59.678 2209 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.11 % Favored : 87.50 % Rotamer: Outliers : 7.33 % Allowed : 27.04 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 3.92 % 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: -3.69 (0.18), residues: 1776 helix: -1.48 (0.94), residues: 31 sheet: -1.12 (0.20), residues: 680 loop : -3.60 (0.16), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 19 TYR 0.011 0.001 TYR J 197 PHE 0.020 0.001 PHE C 117 TRP 0.014 0.001 TRP I 40 HIS 0.003 0.001 HIS J 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13988) covalent geometry : angle 0.64230 / 0.33 (19092) SS BOND : bond 0.00179 / 0.12 ( 22) SS BOND : angle 1.00722 / 0.68 ( 44) hydrogen bonds : bond 0.03204 / 2.09 ( 289) hydrogen bonds : angle 5.44098 / 3.72 ( 717) link_BETA1-4 : bond 0.00114 / 0.05 ( 2) link_BETA1-4 : angle 2.54144 / 1.40 ( 6) link_BETA1-6 : bond 0.00554 / 0.27 ( 2) link_BETA1-6 : angle 1.37180 / 0.75 ( 6) link_NAG-ASN : bond 0.00543 / 0.27 ( 2) link_NAG-ASN : angle 4.53575 / 2.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 163 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: C 34 MET cc_start: 0.5897 (mmm) cc_final: 0.5163 (mmm) REVERT: C 120 TRP cc_start: 0.5564 (m100) cc_final: 0.4421 (m100) REVERT: D 34 MET cc_start: 0.6248 (mmm) cc_final: 0.5918 (mmt) REVERT: D 56 ASP cc_start: 0.3551 (OUTLIER) cc_final: 0.2871 (p0) REVERT: D 97 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.6924 (t) REVERT: F 50 SER cc_start: 0.7541 (p) cc_final: 0.7335 (p) REVERT: F 104 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7834 (mm-40) REVERT: F 131 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7516 (mpt180) REVERT: F 184 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.4550 (t80) REVERT: F 413 ARG cc_start: 0.8046 (mtt90) cc_final: 0.6913 (mtp180) REVERT: F 425 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7396 (pp) REVERT: G 78 THR cc_start: 0.8099 (p) cc_final: 0.7770 (p) REVERT: I 54 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.4044 (m-10) REVERT: J 75 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7572 (mm-40) REVERT: J 102 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7589 (mpt180) REVERT: J 155 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.4446 (t80) REVERT: J 248 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4477 (pp) REVERT: J 378 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8072 (mm-30) REVERT: J 384 ARG cc_start: 0.8106 (mtt90) cc_final: 0.6912 (mtp180) REVERT: J 414 SER cc_start: 0.8167 (t) cc_final: 0.7890 (t) REVERT: M 100 PHE cc_start: 0.4498 (p90) cc_final: 0.4142 (p90) REVERT: N 54 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5039 (m-80) outliers start: 106 outliers final: 71 residues processed: 247 average time/residue: 0.1113 time to fit residues: 41.3458 Evaluate side-chains 237 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 156 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 110 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 126 optimal weight: 0.4980 chunk 158 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.209009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.161346 restraints weight = 14943.880| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.66 r_work: 0.3572 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14016 Z= 0.111 Angle : 0.636 11.969 19154 Z= 0.319 Chirality : 0.048 0.462 2172 Planarity : 0.005 0.062 2450 Dihedral : 7.617 59.137 2190 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.82 % Favored : 87.78 % Rotamer: Outliers : 7.12 % Allowed : 27.25 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.57 (0.18), residues: 1776 helix: -1.36 (0.88), residues: 37 sheet: -1.01 (0.20), residues: 684 loop : -3.58 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.021 0.001 TYR N 91 PHE 0.018 0.001 PHE C 117 TRP 0.015 0.001 TRP I 40 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13988) covalent geometry : angle 0.62961 / 0.32 (19092) SS BOND : bond 0.00150 / 0.11 ( 22) SS BOND : angle 0.96305 / 0.64 ( 44) hydrogen bonds : bond 0.02977 / 1.95 ( 289) hydrogen bonds : angle 5.24249 / 3.57 ( 717) link_BETA1-4 : bond 0.00148 / 0.07 ( 2) link_BETA1-4 : angle 1.91964 / 1.05 ( 6) link_BETA1-6 : bond 0.00152 / 0.07 ( 2) link_BETA1-6 : angle 1.29205 / 0.69 ( 6) link_NAG-ASN : bond 0.00522 / 0.26 ( 2) link_NAG-ASN : angle 4.30028 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 164 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.5984 (mmm) cc_final: 0.5358 (mmm) REVERT: C 35 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.6130 (m90) REVERT: C 95 PHE cc_start: 0.7228 (m-80) cc_final: 0.6922 (m-10) REVERT: C 120 TRP cc_start: 0.5378 (m100) cc_final: 0.4758 (m100) REVERT: C 122 GLN cc_start: 0.5254 (mp10) cc_final: 0.4781 (mp10) REVERT: D 34 MET cc_start: 0.6241 (mmm) cc_final: 0.5890 (mmt) REVERT: D 56 ASP cc_start: 0.3319 (OUTLIER) cc_final: 0.2719 (p0) REVERT: D 97 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7150 (t) REVERT: F 104 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7737 (mm-40) REVERT: F 131 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7578 (mpt180) REVERT: F 184 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.4488 (t80) REVERT: F 247 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7104 (mmtm) REVERT: F 277 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.4208 (pp) REVERT: F 413 ARG cc_start: 0.8018 (mtt90) cc_final: 0.6942 (mtp180) REVERT: F 425 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (pp) REVERT: I 54 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.3945 (m-10) REVERT: J 75 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7522 (mm-40) REVERT: J 102 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7607 (mpt180) REVERT: J 155 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.4427 (t80) REVERT: J 248 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4479 (pp) REVERT: J 378 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8059 (mm-30) REVERT: J 384 ARG cc_start: 0.8089 (mtt90) cc_final: 0.6957 (mtp180) REVERT: J 414 SER cc_start: 0.8241 (t) cc_final: 0.7909 (t) REVERT: M 100 PHE cc_start: 0.4335 (p90) cc_final: 0.3885 (p90) REVERT: N 35 ASN cc_start: 0.7190 (m-40) cc_final: 0.6811 (m-40) REVERT: N 54 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5096 (m-80) outliers start: 103 outliers final: 71 residues processed: 248 average time/residue: 0.1111 time to fit residues: 41.2595 Evaluate side-chains 239 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 155 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 156 GLN ** F 406 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 = 0.4275 r_free = 0.4275 target = 0.205106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157402 restraints weight = 14925.922| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.50 r_work: 0.3540 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14016 Z= 0.164 Angle : 0.680 11.628 19154 Z= 0.345 Chirality : 0.050 0.436 2172 Planarity : 0.005 0.068 2450 Dihedral : 7.531 59.351 2190 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.30 % Favored : 85.30 % Rotamer: Outliers : 7.26 % Allowed : 26.63 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.59 (0.19), residues: 1776 helix: -1.22 (0.94), residues: 30 sheet: -0.97 (0.20), residues: 689 loop : -3.64 (0.16), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.032 0.002 TYR I 91 PHE 0.018 0.002 PHE D 117 TRP 0.019 0.002 TRP I 40 HIS 0.005 0.001 HIS J 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 (13988) covalent geometry : angle 0.67468 / 0.34 (19092) SS BOND : bond 0.00260 / 0.19 ( 22) SS BOND : angle 1.03954 / 0.71 ( 44) hydrogen bonds : bond 0.03508 / 2.29 ( 289) hydrogen bonds : angle 5.27513 / 3.60 ( 717) link_BETA1-4 : bond 0.00437 / 0.22 ( 2) link_BETA1-4 : angle 1.62735 / 0.87 ( 6) link_BETA1-6 : bond 0.00059 / 0.03 ( 2) link_BETA1-6 : angle 1.79029 / 0.96 ( 6) link_NAG-ASN : bond 0.00377 / 0.19 ( 2) link_NAG-ASN : angle 3.94792 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 159 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.6024 (mmm) cc_final: 0.5338 (mmm) REVERT: C 95 PHE cc_start: 0.7349 (m-80) cc_final: 0.6987 (m-10) REVERT: C 120 TRP cc_start: 0.5527 (m100) cc_final: 0.5184 (m100) REVERT: C 122 GLN cc_start: 0.5433 (mp10) cc_final: 0.4945 (mp10) REVERT: D 34 MET cc_start: 0.6336 (mmm) cc_final: 0.6003 (mmt) REVERT: D 56 ASP cc_start: 0.3143 (OUTLIER) cc_final: 0.2600 (p0) REVERT: D 97 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7253 (t) REVERT: D 122 GLN cc_start: 0.5552 (mp10) cc_final: 0.5176 (mp10) REVERT: F 104 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7776 (mm-40) REVERT: F 184 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.4210 (t80) REVERT: F 247 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7174 (mmtm) REVERT: F 249 GLN cc_start: 0.7350 (tp40) cc_final: 0.7008 (tp-100) REVERT: F 277 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.4191 (pp) REVERT: F 413 ARG cc_start: 0.8123 (mtt90) cc_final: 0.6966 (mtp180) REVERT: F 425 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7402 (pp) REVERT: I 54 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.4008 (m-10) REVERT: J 28 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.6249 (tptt) REVERT: J 102 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7550 (mpt180) REVERT: J 155 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.4411 (t80) REVERT: J 248 LEU cc_start: 0.4722 (OUTLIER) cc_final: 0.4351 (pp) REVERT: J 384 ARG cc_start: 0.8183 (mtt90) cc_final: 0.6941 (mtp180) REVERT: J 414 SER cc_start: 0.8197 (t) cc_final: 0.7872 (t) REVERT: M 100 PHE cc_start: 0.4320 (p90) cc_final: 0.4055 (p90) REVERT: N 54 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5113 (m-80) outliers start: 105 outliers final: 85 residues processed: 245 average time/residue: 0.1093 time to fit residues: 40.4125 Evaluate side-chains 254 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 157 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 154 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 268 ASN ** F 406 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 = 0.4270 r_free = 0.4270 target = 0.204880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157080 restraints weight = 14952.954| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.51 r_work: 0.3522 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14016 Z= 0.146 Angle : 0.651 9.621 19154 Z= 0.331 Chirality : 0.048 0.402 2172 Planarity : 0.005 0.067 2450 Dihedral : 7.200 59.336 2186 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.18 % Favored : 86.43 % Rotamer: Outliers : 7.33 % Allowed : 27.04 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.55 (0.19), residues: 1776 helix: -1.62 (0.85), residues: 30 sheet: -0.90 (0.21), residues: 654 loop : -3.56 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.015 0.002 TYR J 197 PHE 0.018 0.001 PHE D 117 TRP 0.020 0.002 TRP I 40 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13988) covalent geometry : angle 0.64603 / 0.33 (19092) SS BOND : bond 0.00202 / 0.14 ( 22) SS BOND : angle 1.01955 / 0.68 ( 44) hydrogen bonds : bond 0.03255 / 2.13 ( 289) hydrogen bonds : angle 5.21551 / 3.56 ( 717) link_BETA1-4 : bond 0.00395 / 0.20 ( 2) link_BETA1-4 : angle 1.39332 / 0.72 ( 6) link_BETA1-6 : bond 0.00169 / 0.09 ( 2) link_BETA1-6 : angle 1.80458 / 0.96 ( 6) link_NAG-ASN : bond 0.00400 / 0.20 ( 2) link_NAG-ASN : angle 3.50507 / 1.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 160 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.5876 (mmm) cc_final: 0.5210 (mmm) REVERT: C 95 PHE cc_start: 0.7367 (m-80) cc_final: 0.7037 (m-10) REVERT: C 97 VAL cc_start: 0.6643 (p) cc_final: 0.5764 (m) REVERT: C 122 GLN cc_start: 0.5367 (mp10) cc_final: 0.4879 (mp10) REVERT: D 34 MET cc_start: 0.6162 (mmm) cc_final: 0.5798 (mmt) REVERT: D 56 ASP cc_start: 0.3101 (OUTLIER) cc_final: 0.2567 (p0) REVERT: D 97 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7173 (t) REVERT: D 122 GLN cc_start: 0.5405 (mp10) cc_final: 0.5048 (mp10) REVERT: F 57 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.6168 (tptt) REVERT: F 131 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7588 (mpt180) REVERT: F 184 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.4142 (t80) REVERT: F 249 GLN cc_start: 0.7326 (tp40) cc_final: 0.7043 (tp-100) REVERT: F 270 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7221 (mm) REVERT: F 277 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4264 (pp) REVERT: F 413 ARG cc_start: 0.8133 (mtt90) cc_final: 0.6994 (mtp180) REVERT: F 425 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7409 (pp) REVERT: J 102 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7614 (mpt180) REVERT: J 155 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.4246 (t80) REVERT: J 248 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4339 (pp) REVERT: J 378 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8126 (mm-30) REVERT: J 384 ARG cc_start: 0.8261 (mtt90) cc_final: 0.7021 (mtp180) REVERT: J 414 SER cc_start: 0.8185 (t) cc_final: 0.7860 (t) REVERT: M 100 PHE cc_start: 0.4293 (p90) cc_final: 0.4041 (p90) REVERT: N 54 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5221 (m-80) outliers start: 106 outliers final: 81 residues processed: 247 average time/residue: 0.0960 time to fit residues: 35.9359 Evaluate side-chains 251 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 158 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 143 optimal weight: 0.0270 chunk 16 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.204763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158004 restraints weight = 14791.742| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.39 r_work: 0.3538 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14016 Z= 0.148 Angle : 0.655 11.176 19154 Z= 0.333 Chirality : 0.048 0.367 2172 Planarity : 0.005 0.075 2450 Dihedral : 7.129 59.563 2184 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.02 % Favored : 85.59 % Rotamer: Outliers : 7.26 % Allowed : 26.69 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.44 (0.19), residues: 1776 helix: -1.41 (0.87), residues: 30 sheet: -0.72 (0.21), residues: 662 loop : -3.58 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 264 TYR 0.016 0.002 TYR J 197 PHE 0.017 0.001 PHE D 117 TRP 0.022 0.002 TRP I 40 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (13988) covalent geometry : angle 0.64966 / 0.33 (19092) SS BOND : bond 0.00231 / 0.16 ( 22) SS BOND : angle 1.22349 / 0.77 ( 44) hydrogen bonds : bond 0.03290 / 2.13 ( 289) hydrogen bonds : angle 5.18267 / 3.54 ( 717) link_BETA1-4 : bond 0.00532 / 0.27 ( 2) link_BETA1-4 : angle 1.41721 / 0.70 ( 6) link_BETA1-6 : bond 0.00384 / 0.19 ( 2) link_BETA1-6 : angle 1.87535 / 0.97 ( 6) link_NAG-ASN : bond 0.00374 / 0.19 ( 2) link_NAG-ASN : angle 3.07968 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 162 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.5961 (mmm) cc_final: 0.5258 (mmm) REVERT: C 83 MET cc_start: 0.3770 (OUTLIER) cc_final: 0.0434 (mpt) REVERT: D 56 ASP cc_start: 0.2993 (OUTLIER) cc_final: 0.2461 (p0) REVERT: D 97 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7323 (t) REVERT: D 122 GLN cc_start: 0.5572 (mp10) cc_final: 0.5217 (mp10) REVERT: F 57 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6245 (tptt) REVERT: F 184 TYR cc_start: 0.5803 (OUTLIER) cc_final: 0.4109 (t80) REVERT: F 249 GLN cc_start: 0.7283 (tp40) cc_final: 0.7001 (tp-100) REVERT: F 270 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7334 (mm) REVERT: F 277 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4327 (pp) REVERT: F 413 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7108 (mtp180) REVERT: F 425 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7417 (pp) REVERT: I 54 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.3914 (m-10) REVERT: J 28 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6315 (tptt) REVERT: J 102 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7555 (mpt180) REVERT: J 155 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.4221 (t80) REVERT: J 248 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4345 (pp) REVERT: J 378 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8059 (mm-30) REVERT: J 384 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7075 (mtp180) REVERT: J 414 SER cc_start: 0.8217 (t) cc_final: 0.7892 (t) REVERT: M 100 PHE cc_start: 0.4270 (p90) cc_final: 0.4042 (p90) REVERT: N 54 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: N 79 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7772 (mmtm) outliers start: 105 outliers final: 84 residues processed: 248 average time/residue: 0.1039 time to fit residues: 38.8346 Evaluate side-chains 261 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 162 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 184 TYR Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 162 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.202069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154045 restraints weight = 14882.045| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.48 r_work: 0.3458 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14016 Z= 0.204 Angle : 0.710 9.205 19154 Z= 0.364 Chirality : 0.050 0.336 2172 Planarity : 0.005 0.078 2450 Dihedral : 7.376 59.865 2184 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.43 % Favored : 84.29 % Rotamer: Outliers : 7.26 % Allowed : 27.32 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.57 (0.19), residues: 1776 helix: -1.14 (0.87), residues: 28 sheet: -0.99 (0.21), residues: 673 loop : -3.56 (0.16), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 362 TYR 0.021 0.002 TYR J 197 PHE 0.021 0.002 PHE D 117 TRP 0.031 0.002 TRP I 40 HIS 0.006 0.002 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.20 (13988) covalent geometry : angle 0.70589 / 0.36 (19092) SS BOND : bond 0.00299 / 0.21 ( 22) SS BOND : angle 1.21219 / 0.79 ( 44) hydrogen bonds : bond 0.03811 / 2.48 ( 289) hydrogen bonds : angle 5.32384 / 3.63 ( 717) link_BETA1-4 : bond 0.00668 / 0.33 ( 2) link_BETA1-4 : angle 1.41929 / 0.71 ( 6) link_BETA1-6 : bond 0.00642 / 0.32 ( 2) link_BETA1-6 : angle 1.91212 / 1.00 ( 6) link_NAG-ASN : bond 0.00090 / 0.05 ( 2) link_NAG-ASN : angle 2.58501 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 158 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 GLN cc_start: 0.5526 (mp10) cc_final: 0.5118 (mp10) REVERT: D 56 ASP cc_start: 0.2986 (OUTLIER) cc_final: 0.2714 (p0) REVERT: D 97 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7416 (t) REVERT: D 122 GLN cc_start: 0.5537 (mp10) cc_final: 0.5164 (mp10) REVERT: F 57 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.6222 (tptt) REVERT: F 247 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7164 (mmtp) REVERT: F 249 GLN cc_start: 0.7260 (tp40) cc_final: 0.6957 (tp40) REVERT: F 277 LEU cc_start: 0.4820 (OUTLIER) cc_final: 0.4309 (pp) REVERT: F 307 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8539 (pttp) REVERT: F 413 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7128 (mtp180) REVERT: F 425 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7373 (pp) REVERT: J 28 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.6371 (tptt) REVERT: J 155 TYR cc_start: 0.5442 (OUTLIER) cc_final: 0.3814 (t80) REVERT: J 248 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4351 (pp) REVERT: J 384 ARG cc_start: 0.8401 (mtt90) cc_final: 0.7168 (mtp180) REVERT: J 414 SER cc_start: 0.8278 (t) cc_final: 0.7974 (t) REVERT: M 100 PHE cc_start: 0.4365 (p90) cc_final: 0.4144 (p90) REVERT: N 33 ASP cc_start: 0.6833 (t0) cc_final: 0.6617 (t0) REVERT: N 54 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.4459 (m-10) REVERT: N 79 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7661 (mmtm) outliers start: 105 outliers final: 84 residues processed: 244 average time/residue: 0.0938 time to fit residues: 34.7617 Evaluate side-chains 251 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 155 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 251 ILE Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 310 THR Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 254 GLN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.202558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154121 restraints weight = 14816.725| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.48 r_work: 0.3518 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14016 Z= 0.216 Angle : 0.735 11.389 19154 Z= 0.374 Chirality : 0.050 0.309 2172 Planarity : 0.006 0.080 2450 Dihedral : 7.400 59.213 2182 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.15 % Favored : 84.57 % Rotamer: Outliers : 6.92 % Allowed : 27.80 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.69 (0.18), residues: 1776 helix: -1.07 (0.90), residues: 28 sheet: -1.15 (0.21), residues: 681 loop : -3.59 (0.16), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 265 TYR 0.021 0.002 TYR J 197 PHE 0.019 0.002 PHE D 117 TRP 0.025 0.002 TRP G 111 HIS 0.005 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (13988) covalent geometry : angle 0.73094 / 0.37 (19092) SS BOND : bond 0.00338 / 0.24 ( 22) SS BOND : angle 1.45615 / 0.96 ( 44) hydrogen bonds : bond 0.03851 / 2.51 ( 289) hydrogen bonds : angle 5.38517 / 3.66 ( 717) link_BETA1-4 : bond 0.00703 / 0.35 ( 2) link_BETA1-4 : angle 1.53382 / 0.78 ( 6) link_BETA1-6 : bond 0.00493 / 0.24 ( 2) link_BETA1-6 : angle 1.96012 / 1.00 ( 6) link_NAG-ASN : bond 0.00137 / 0.07 ( 2) link_NAG-ASN : angle 2.24578 / 1.24 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 153 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.6072 (mmm) cc_final: 0.5594 (mmm) REVERT: C 122 GLN cc_start: 0.5422 (mp10) cc_final: 0.4990 (mp10) REVERT: D 34 MET cc_start: 0.6116 (mmm) cc_final: 0.5805 (mmt) REVERT: D 56 ASP cc_start: 0.3059 (OUTLIER) cc_final: 0.2746 (p0) REVERT: D 97 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7430 (t) REVERT: D 122 GLN cc_start: 0.5664 (mp10) cc_final: 0.5287 (mp10) REVERT: F 57 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.6432 (tptt) REVERT: F 77 ASP cc_start: 0.7615 (t0) cc_final: 0.7392 (t0) REVERT: F 247 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7166 (mmtp) REVERT: F 249 GLN cc_start: 0.7308 (tp40) cc_final: 0.7011 (tp-100) REVERT: F 277 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4391 (pp) REVERT: F 307 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8590 (pttp) REVERT: F 413 ARG cc_start: 0.8402 (mtt90) cc_final: 0.7256 (mtp180) REVERT: F 425 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7449 (pp) REVERT: J 28 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.6503 (tptt) REVERT: J 155 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.3771 (t80) REVERT: J 248 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4390 (pp) REVERT: J 378 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8126 (mm-30) REVERT: J 384 ARG cc_start: 0.8502 (mtt90) cc_final: 0.7272 (mtp180) REVERT: J 414 SER cc_start: 0.8279 (t) cc_final: 0.8007 (t) REVERT: N 54 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.4750 (m-10) REVERT: N 79 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7730 (mmtm) outliers start: 100 outliers final: 86 residues processed: 234 average time/residue: 0.0979 time to fit residues: 34.6114 Evaluate side-chains 247 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 149 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 155 TYR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 251 ILE Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 310 THR Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 400 ASN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 92 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 268 ASN ** F 406 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 = 0.4269 r_free = 0.4269 target = 0.205035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156851 restraints weight = 14892.315| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.56 r_work: 0.3542 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14016 Z= 0.110 Angle : 0.631 8.712 19154 Z= 0.320 Chirality : 0.046 0.294 2172 Planarity : 0.005 0.079 2450 Dihedral : 6.892 59.277 2180 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.88 % Favored : 87.84 % Rotamer: Outliers : 5.53 % Allowed : 29.18 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -3.49 (0.19), residues: 1776 helix: -0.60 (0.92), residues: 34 sheet: -0.93 (0.21), residues: 662 loop : -3.51 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 19 TYR 0.016 0.001 TYR I 92 PHE 0.015 0.001 PHE C 117 TRP 0.016 0.001 TRP I 40 HIS 0.002 0.001 HIS F 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (13988) covalent geometry : angle 0.62758 / 0.32 (19092) SS BOND : bond 0.00156 / 0.11 ( 22) SS BOND : angle 1.17578 / 0.77 ( 44) hydrogen bonds : bond 0.02997 / 1.95 ( 289) hydrogen bonds : angle 5.12753 / 3.51 ( 717) link_BETA1-4 : bond 0.00542 / 0.28 ( 2) link_BETA1-4 : angle 1.44771 / 0.75 ( 6) link_BETA1-6 : bond 0.00134 / 0.07 ( 2) link_BETA1-6 : angle 1.56817 / 0.79 ( 6) link_NAG-ASN : bond 0.00429 / 0.22 ( 2) link_NAG-ASN : angle 2.05594 / 1.13 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.64 seconds wall clock time: 65 minutes 37.78 seconds (3937.78 seconds total)