Starting phenix.real_space_refine on Wed Mar 4 05:20:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ncn_49260/03_2026/9ncn_49260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ncn_49260/03_2026/9ncn_49260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ncn_49260/03_2026/9ncn_49260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ncn_49260/03_2026/9ncn_49260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ncn_49260/03_2026/9ncn_49260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ncn_49260/03_2026/9ncn_49260.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 94 5.16 5 C 6800 2.51 5 N 1826 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10722 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 176 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 176 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "H" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "E" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4873 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 571} Chain breaks: 4 Chain: "F" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4873 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 571} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.49, per 1000 atoms: 0.23 Number of scatterers: 10722 At special positions: 0 Unit cell: (82.467, 149.107, 86.632, 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 94 16.00 O 2002 8.00 N 1826 7.00 C 6800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS G 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS H 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS H 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.02 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " 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 A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 1 " - " ASN E 111 " " NAG B 1 " - " ASN F 111 " " NAG E1001 " - " ASN E 25 " " NAG E1002 " - " ASN E 397 " " NAG E1003 " - " ASN E 215 " " NAG F1001 " - " ASN F 397 " " NAG F1002 " - " ASN F 25 " " NAG F1003 " - " ASN F 215 " TRANS " DHI C 24 " - " GLY C 23 " " DHI D 24 " - " GLY D 23 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 371.4 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DHI C 24 " pdb=" CB DHI D 24 " Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 24 sheets defined 20.2% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.127A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 69 through 75 Processing helix chain 'D' and resid 8 through 20 removed outlier: 4.128A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'E' and resid 16 through 26 removed outlier: 4.171A pdb=" N ARG E 19 " --> pdb=" O ASN E 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN E 25 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 3.755A pdb=" N PHE E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.603A pdb=" N ASP E 151 " --> pdb=" O ASN E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 200 Processing helix chain 'E' and resid 255 through 265 Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.872A pdb=" N GLU E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 359 Processing helix chain 'E' and resid 435 through 446 removed outlier: 4.259A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 443 " --> pdb=" O ILE E 439 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 692 through 714 removed outlier: 3.752A pdb=" N LEU E 696 " --> pdb=" O ILE E 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 26 removed outlier: 3.567A pdb=" N ARG F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN F 25 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.735A pdb=" N PHE F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.595A pdb=" N ASN F 143 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 196 through 200 Processing helix chain 'F' and resid 255 through 268 Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.905A pdb=" N GLU F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 359 Processing helix chain 'F' and resid 435 through 446 removed outlier: 4.216A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 692 through 714 removed outlier: 3.677A pdb=" N GLU F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 9 through 13 removed outlier: 8.605A pdb=" N GLN E 34 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 9 through 13 removed outlier: 8.605A pdb=" N GLN E 34 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU E 62 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR E 91 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ARG E 118 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'E' and resid 212 through 216 removed outlier: 5.463A pdb=" N LEU E 213 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N CYS E 228 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN E 215 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA9, first strand: chain 'E' and resid 311 through 312 Processing sheet with id=AB1, first strand: chain 'E' and resid 318 through 321 removed outlier: 6.404A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N HIS E 429 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA E 402 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 471 through 472 removed outlier: 6.329A pdb=" N GLU E 471 " --> pdb=" O LYS E 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AB4, first strand: chain 'E' and resid 530 through 534 Processing sheet with id=AB5, first strand: chain 'F' and resid 9 through 13 removed outlier: 8.556A pdb=" N GLN F 34 " --> pdb=" O PRO F 9 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET F 11 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU F 36 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE F 13 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET F 38 " --> pdb=" O ILE F 13 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 9 through 13 removed outlier: 8.556A pdb=" N GLN F 34 " --> pdb=" O PRO F 9 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET F 11 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU F 36 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE F 13 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET F 38 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LEU F 62 " --> pdb=" O GLY F 31 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU F 33 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE F 64 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE F 35 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL F 66 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU F 37 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR F 91 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ARG F 118 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 146 " --> pdb=" O ILE F 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AB8, first strand: chain 'F' and resid 212 through 216 removed outlier: 5.369A pdb=" N LEU F 213 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N CYS F 228 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN F 215 " --> pdb=" O VAL F 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AC1, first strand: chain 'F' and resid 252 through 254 removed outlier: 6.394A pdb=" N HIS F 247 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC3, first strand: chain 'F' and resid 311 through 312 Processing sheet with id=AC4, first strand: chain 'F' and resid 318 through 321 removed outlier: 6.347A pdb=" N LEU F 340 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG F 371 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE F 342 " --> pdb=" O ARG F 371 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS F 425 " --> pdb=" O TYR F 398 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AC6, first strand: chain 'F' and resid 530 through 534 252 hydrogen bonds defined for protein. 606 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: 1.76 Time building geometry restraints manager: 0.90 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: 3454 1.34 - 1.46: 2518 1.46 - 1.58: 4886 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 10970 Sorted by residual: bond pdb=" CB VAL E 531 " pdb=" CG2 VAL E 531 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CA ASP E 542 " pdb=" C ASP E 542 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 8.86e-01 bond pdb=" C ASP F 542 " pdb=" N PRO F 543 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.62e-01 bond pdb=" N ASP E 533 " pdb=" CA ASP E 533 " ideal model delta sigma weight residual 1.454 1.466 -0.012 1.31e-02 5.83e+03 8.46e-01 bond pdb=" N ASN F 470 " pdb=" CA ASN F 470 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.54e-02 4.22e+03 7.28e-01 ... (remaining 10965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 14344 1.86 - 3.72: 455 3.72 - 5.57: 39 5.57 - 7.43: 9 7.43 - 9.29: 3 Bond angle restraints: 14850 Sorted by residual: angle pdb=" N ASP E 542 " pdb=" CA ASP E 542 " pdb=" C ASP E 542 " ideal model delta sigma weight residual 109.81 119.10 -9.29 2.21e+00 2.05e-01 1.77e+01 angle pdb=" N ASP F 542 " pdb=" CA ASP F 542 " pdb=" C ASP F 542 " ideal model delta sigma weight residual 109.81 117.55 -7.74 2.21e+00 2.05e-01 1.23e+01 angle pdb=" N CYS F 8 " pdb=" CA CYS F 8 " pdb=" C CYS F 8 " ideal model delta sigma weight residual 109.81 117.02 -7.21 2.21e+00 2.05e-01 1.06e+01 angle pdb=" N CYS E 8 " pdb=" CA CYS E 8 " pdb=" C CYS E 8 " ideal model delta sigma weight residual 109.81 116.47 -6.66 2.21e+00 2.05e-01 9.07e+00 angle pdb=" N ASP F 322 " pdb=" CA ASP F 322 " pdb=" C ASP F 322 " ideal model delta sigma weight residual 114.64 110.43 4.21 1.52e+00 4.33e-01 7.66e+00 ... (remaining 14845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 6151 17.12 - 34.24: 491 34.24 - 51.36: 107 51.36 - 68.48: 23 68.48 - 85.60: 10 Dihedral angle restraints: 6782 sinusoidal: 2970 harmonic: 3812 Sorted by residual: dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 155 " pdb=" CB CYS F 155 " ideal model delta sinusoidal sigma weight residual -86.00 -138.54 52.54 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CA LEU F 36 " pdb=" C LEU F 36 " pdb=" N LEU F 37 " pdb=" CA LEU F 37 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 6779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1273 0.054 - 0.109: 293 0.109 - 0.163: 76 0.163 - 0.218: 4 0.218 - 0.272: 2 Chirality restraints: 1648 Sorted by residual: chirality pdb=" C2 NAG B 1 " pdb=" C1 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" N2 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.22 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN E 111 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C1 NAG F1002 " pdb=" ND2 ASN F 25 " pdb=" C2 NAG F1002 " pdb=" O5 NAG F1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1645 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 576 " 0.206 9.50e-02 1.11e+02 9.32e-02 6.78e+00 pdb=" NE ARG F 576 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 576 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG F 576 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 576 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 83 " -0.202 9.50e-02 1.11e+02 9.11e-02 6.51e+00 pdb=" NE ARG E 83 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 83 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG E 83 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 83 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 42 " -0.187 9.50e-02 1.11e+02 8.47e-02 5.73e+00 pdb=" NE ARG F 42 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG F 42 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG F 42 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 42 " -0.000 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 3507 2.85 - 3.36: 9857 3.36 - 3.87: 17556 3.87 - 4.39: 20850 4.39 - 4.90: 34770 Nonbonded interactions: 86540 Sorted by model distance: nonbonded pdb=" NZ LYS E 121 " pdb=" OE2 GLU F 706 " model vdw 2.335 3.120 nonbonded pdb=" O PRO F 77 " pdb=" ND2 ASN F 108 " model vdw 2.395 3.120 nonbonded pdb=" NE ARG F 65 " pdb=" OE1 GLU F 97 " model vdw 2.397 3.120 nonbonded pdb=" OD1 ASP E 413 " pdb=" OG SER E 415 " model vdw 2.422 3.040 nonbonded pdb=" O PRO F 52 " pdb=" ND2 ASN F 78 " model vdw 2.433 3.120 ... (remaining 86535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 0.035 11016 Z= 0.137 Angle : 0.770 11.472 14954 Z= 0.412 Chirality : 0.050 0.272 1648 Planarity : 0.008 0.093 1896 Dihedral : 13.334 85.602 4214 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.99 % Favored : 92.86 % Rotamer: Outliers : 1.42 % Allowed : 3.51 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1274 helix: -2.12 (0.29), residues: 178 sheet: -0.91 (0.44), residues: 138 loop : -0.97 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG F 576 TYR 0.022 0.003 TYR F 367 PHE 0.022 0.002 PHE E 427 TRP 0.027 0.003 TRP E 529 HIS 0.005 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00288 (10970) covalent geometry : angle 0.74292 (14850) SS BOND : bond 0.00340 ( 34) SS BOND : angle 1.00241 ( 68) hydrogen bonds : bond 0.20095 ( 252) hydrogen bonds : angle 9.07659 ( 606) link_BETA1-4 : bond 0.00763 ( 2) link_BETA1-4 : angle 4.22067 ( 6) link_NAG-ASN : bond 0.00399 ( 8) link_NAG-ASN : angle 4.48740 ( 24) link_TRANS : bond 0.00047 ( 2) link_TRANS : angle 0.68080 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 250 ASP cc_start: 0.8222 (t0) cc_final: 0.8018 (t0) REVERT: E 294 MET cc_start: 0.6611 (ttt) cc_final: 0.6010 (pmm) REVERT: E 430 TYR cc_start: 0.7278 (m-80) cc_final: 0.6770 (m-80) REVERT: E 587 TYR cc_start: 0.8022 (m-80) cc_final: 0.7662 (m-80) REVERT: F 294 MET cc_start: 0.6499 (ttt) cc_final: 0.6058 (pmm) REVERT: F 430 TYR cc_start: 0.7280 (m-80) cc_final: 0.6793 (m-80) outliers start: 17 outliers final: 4 residues processed: 255 average time/residue: 0.5467 time to fit residues: 150.7075 Evaluate side-chains 135 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain F residue 275 HIS Chi-restraints excluded: chain F residue 512 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN F 230 ASN F 282 ASN F 343 ASN F 348 ASN F 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.165944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.132408 restraints weight = 21451.766| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 4.11 r_work: 0.4031 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11016 Z= 0.148 Angle : 0.799 21.238 14954 Z= 0.392 Chirality : 0.050 0.286 1648 Planarity : 0.004 0.041 1896 Dihedral : 8.449 56.690 1644 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 13.29 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.23), residues: 1274 helix: -1.26 (0.35), residues: 182 sheet: -0.59 (0.35), residues: 182 loop : -0.63 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 47 TYR 0.011 0.001 TYR E 374 PHE 0.023 0.002 PHE F 256 TRP 0.014 0.002 TRP E 133 HIS 0.020 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00334 (10970) covalent geometry : angle 0.75265 (14850) SS BOND : bond 0.00378 ( 34) SS BOND : angle 1.22642 ( 68) hydrogen bonds : bond 0.04947 ( 252) hydrogen bonds : angle 6.95307 ( 606) link_BETA1-4 : bond 0.00663 ( 2) link_BETA1-4 : angle 4.70014 ( 6) link_NAG-ASN : bond 0.00675 ( 8) link_NAG-ASN : angle 6.14378 ( 24) link_TRANS : bond 0.00139 ( 2) link_TRANS : angle 0.40612 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8224 (mp) REVERT: E 23 LEU cc_start: 0.6793 (tt) cc_final: 0.6536 (mp) REVERT: E 132 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: E 250 ASP cc_start: 0.8427 (t0) cc_final: 0.8142 (t0) REVERT: E 294 MET cc_start: 0.6651 (ttt) cc_final: 0.6278 (pmm) REVERT: E 322 ASP cc_start: 0.7894 (p0) cc_final: 0.7291 (t0) REVERT: E 353 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7804 (pm20) REVERT: E 430 TYR cc_start: 0.7197 (m-80) cc_final: 0.6389 (m-80) REVERT: E 474 LYS cc_start: 0.8706 (tmmt) cc_final: 0.8298 (pptt) REVERT: E 587 TYR cc_start: 0.7833 (m-80) cc_final: 0.7633 (m-80) REVERT: F 124 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6493 (tt0) REVERT: F 177 GLN cc_start: 0.9051 (pt0) cc_final: 0.8594 (pm20) REVERT: F 322 ASP cc_start: 0.8002 (p0) cc_final: 0.7294 (t0) REVERT: F 343 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7407 (t0) REVERT: F 353 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: F 430 TYR cc_start: 0.6985 (m-80) cc_final: 0.6267 (m-80) REVERT: F 504 MET cc_start: 0.8160 (mpp) cc_final: 0.7940 (mmt) outliers start: 34 outliers final: 12 residues processed: 175 average time/residue: 0.5225 time to fit residues: 99.6538 Evaluate side-chains 145 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 275 HIS Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 512 TYR Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 715 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN F 282 ASN F 343 ASN F 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.164795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.131363 restraints weight = 21646.781| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 4.06 r_work: 0.4046 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11016 Z= 0.152 Angle : 0.755 20.774 14954 Z= 0.367 Chirality : 0.048 0.205 1648 Planarity : 0.004 0.047 1896 Dihedral : 8.131 59.148 1644 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.76 % Allowed : 15.97 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1274 helix: -0.83 (0.36), residues: 172 sheet: -0.78 (0.34), residues: 184 loop : -0.49 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 47 TYR 0.019 0.001 TYR F 107 PHE 0.014 0.002 PHE F 427 TRP 0.012 0.001 TRP F 133 HIS 0.015 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00353 (10970) covalent geometry : angle 0.71239 (14850) SS BOND : bond 0.00321 ( 34) SS BOND : angle 0.96449 ( 68) hydrogen bonds : bond 0.04378 ( 252) hydrogen bonds : angle 6.64632 ( 606) link_BETA1-4 : bond 0.00575 ( 2) link_BETA1-4 : angle 4.40212 ( 6) link_NAG-ASN : bond 0.00893 ( 8) link_NAG-ASN : angle 5.81858 ( 24) link_TRANS : bond 0.00019 ( 2) link_TRANS : angle 0.40095 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 VAL cc_start: 0.6282 (t) cc_final: 0.5890 (t) REVERT: C 4 GLN cc_start: 0.6866 (tp40) cc_final: 0.6396 (pm20) REVERT: D 15 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8298 (mp) REVERT: E 23 LEU cc_start: 0.6956 (tt) cc_final: 0.6742 (mp) REVERT: E 132 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: E 250 ASP cc_start: 0.8373 (t0) cc_final: 0.8073 (t0) REVERT: E 294 MET cc_start: 0.6658 (ttt) cc_final: 0.6299 (pmm) REVERT: E 322 ASP cc_start: 0.7890 (p0) cc_final: 0.7253 (t0) REVERT: E 353 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7892 (mp0) REVERT: E 430 TYR cc_start: 0.7295 (m-80) cc_final: 0.6406 (m-80) REVERT: E 474 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8284 (pptt) REVERT: E 490 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: E 579 TYR cc_start: 0.7308 (m-10) cc_final: 0.7093 (m-80) REVERT: E 587 TYR cc_start: 0.7816 (m-80) cc_final: 0.7561 (m-80) REVERT: F 124 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6916 (mp0) REVERT: F 177 GLN cc_start: 0.9040 (pt0) cc_final: 0.8583 (pm20) REVERT: F 294 MET cc_start: 0.6576 (tmm) cc_final: 0.6049 (tmt) REVERT: F 322 ASP cc_start: 0.8033 (p0) cc_final: 0.7174 (t0) REVERT: F 343 ASN cc_start: 0.7735 (t160) cc_final: 0.7311 (t0) REVERT: F 353 GLU cc_start: 0.7841 (mp0) cc_final: 0.7556 (pm20) REVERT: F 354 LEU cc_start: 0.8019 (mt) cc_final: 0.7805 (mp) REVERT: F 430 TYR cc_start: 0.7022 (m-80) cc_final: 0.6272 (m-80) REVERT: F 474 LYS cc_start: 0.8233 (tptm) cc_final: 0.8007 (tptp) REVERT: F 479 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.6898 (ppt90) outliers start: 33 outliers final: 14 residues processed: 159 average time/residue: 0.5052 time to fit residues: 87.4144 Evaluate side-chains 137 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 275 HIS Chi-restraints excluded: chain F residue 512 TYR Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 715 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN ** E 282 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 = 0.4621 r_free = 0.4621 target = 0.164042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.129716 restraints weight = 21529.407| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 4.17 r_work: 0.3999 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11016 Z= 0.158 Angle : 0.740 19.840 14954 Z= 0.357 Chirality : 0.048 0.183 1648 Planarity : 0.004 0.045 1896 Dihedral : 7.902 59.108 1644 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.76 % Allowed : 14.88 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.23), residues: 1274 helix: -0.78 (0.37), residues: 170 sheet: -0.98 (0.33), residues: 186 loop : -0.49 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 47 TYR 0.013 0.001 TYR F 107 PHE 0.028 0.002 PHE F 256 TRP 0.012 0.001 TRP F 133 HIS 0.013 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00372 (10970) covalent geometry : angle 0.69925 (14850) SS BOND : bond 0.00337 ( 34) SS BOND : angle 1.00362 ( 68) hydrogen bonds : bond 0.04192 ( 252) hydrogen bonds : angle 6.53211 ( 606) link_BETA1-4 : bond 0.00418 ( 2) link_BETA1-4 : angle 4.23450 ( 6) link_NAG-ASN : bond 0.00830 ( 8) link_NAG-ASN : angle 5.56459 ( 24) link_TRANS : bond 0.00021 ( 2) link_TRANS : angle 0.46505 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.6861 (tp40) cc_final: 0.6479 (pm20) REVERT: E 56 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7780 (ttp) REVERT: E 124 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7039 (tt0) REVERT: E 132 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: E 322 ASP cc_start: 0.7910 (p0) cc_final: 0.7177 (t0) REVERT: E 430 TYR cc_start: 0.7280 (m-80) cc_final: 0.6395 (m-80) REVERT: E 474 LYS cc_start: 0.8737 (tmmt) cc_final: 0.8294 (pptt) REVERT: E 490 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: E 579 TYR cc_start: 0.7336 (m-10) cc_final: 0.7118 (m-80) REVERT: E 587 TYR cc_start: 0.7785 (m-80) cc_final: 0.7549 (m-80) REVERT: F 12 ASP cc_start: 0.7796 (p0) cc_final: 0.7549 (p0) REVERT: F 177 GLN cc_start: 0.9044 (pt0) cc_final: 0.8565 (pm20) REVERT: F 322 ASP cc_start: 0.8034 (p0) cc_final: 0.7177 (t0) REVERT: F 353 GLU cc_start: 0.7869 (mp0) cc_final: 0.7560 (pm20) REVERT: F 354 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7651 (mp) REVERT: F 430 TYR cc_start: 0.7061 (m-80) cc_final: 0.6307 (m-80) REVERT: F 474 LYS cc_start: 0.8244 (tptm) cc_final: 0.8038 (tptt) REVERT: F 541 ASN cc_start: 0.8399 (p0) cc_final: 0.7846 (p0) outliers start: 45 outliers final: 17 residues processed: 161 average time/residue: 0.5025 time to fit residues: 88.3332 Evaluate side-chains 135 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 275 HIS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 512 TYR Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 715 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.163437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.128927 restraints weight = 21321.390| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 4.16 r_work: 0.3981 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11016 Z= 0.168 Angle : 0.730 19.465 14954 Z= 0.355 Chirality : 0.047 0.166 1648 Planarity : 0.004 0.035 1896 Dihedral : 7.827 58.787 1642 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.60 % Allowed : 17.39 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1274 helix: -0.72 (0.37), residues: 170 sheet: -1.23 (0.33), residues: 196 loop : -0.50 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 22 TYR 0.014 0.001 TYR E 507 PHE 0.015 0.002 PHE F 428 TRP 0.013 0.001 TRP F 133 HIS 0.011 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00398 (10970) covalent geometry : angle 0.69070 (14850) SS BOND : bond 0.00387 ( 34) SS BOND : angle 0.99732 ( 68) hydrogen bonds : bond 0.04077 ( 252) hydrogen bonds : angle 6.49092 ( 606) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 4.11916 ( 6) link_NAG-ASN : bond 0.00812 ( 8) link_NAG-ASN : angle 5.47247 ( 24) link_TRANS : bond 0.00082 ( 2) link_TRANS : angle 0.40611 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.6866 (tp40) cc_final: 0.6473 (pm20) REVERT: E 56 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: E 124 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7084 (tt0) REVERT: E 132 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: E 294 MET cc_start: 0.6707 (tmm) cc_final: 0.5970 (tmt) REVERT: E 322 ASP cc_start: 0.7944 (p0) cc_final: 0.7109 (t0) REVERT: E 430 TYR cc_start: 0.7330 (m-80) cc_final: 0.6449 (m-80) REVERT: E 474 LYS cc_start: 0.8731 (tmmt) cc_final: 0.8289 (pptt) REVERT: E 490 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: E 579 TYR cc_start: 0.7420 (m-10) cc_final: 0.7194 (m-80) REVERT: E 587 TYR cc_start: 0.7801 (m-80) cc_final: 0.7566 (m-80) REVERT: F 12 ASP cc_start: 0.7976 (p0) cc_final: 0.7768 (p0) REVERT: F 135 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7458 (tpm170) REVERT: F 230 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6969 (m-40) REVERT: F 322 ASP cc_start: 0.8056 (p0) cc_final: 0.7120 (t0) REVERT: F 353 GLU cc_start: 0.7883 (mp0) cc_final: 0.7560 (pm20) REVERT: F 354 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7676 (mp) REVERT: F 430 TYR cc_start: 0.7009 (m-80) cc_final: 0.6220 (m-80) REVERT: F 541 ASN cc_start: 0.8547 (p0) cc_final: 0.8242 (p0) outliers start: 43 outliers final: 18 residues processed: 151 average time/residue: 0.4601 time to fit residues: 76.6211 Evaluate side-chains 133 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 715 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.160754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.126073 restraints weight = 21434.376| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 4.13 r_work: 0.3939 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11016 Z= 0.231 Angle : 0.783 19.323 14954 Z= 0.382 Chirality : 0.049 0.181 1648 Planarity : 0.004 0.030 1896 Dihedral : 7.886 59.594 1638 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.18 % Allowed : 18.06 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.23), residues: 1274 helix: -1.17 (0.35), residues: 184 sheet: -1.43 (0.33), residues: 194 loop : -0.64 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 22 TYR 0.019 0.002 TYR E 374 PHE 0.028 0.003 PHE F 256 TRP 0.015 0.002 TRP F 133 HIS 0.009 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00545 (10970) covalent geometry : angle 0.74422 (14850) SS BOND : bond 0.00507 ( 34) SS BOND : angle 1.20947 ( 68) hydrogen bonds : bond 0.04365 ( 252) hydrogen bonds : angle 6.54846 ( 606) link_BETA1-4 : bond 0.00631 ( 2) link_BETA1-4 : angle 4.40436 ( 6) link_NAG-ASN : bond 0.00844 ( 8) link_NAG-ASN : angle 5.49795 ( 24) link_TRANS : bond 0.00121 ( 2) link_TRANS : angle 0.37090 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.6789 (tp40) cc_final: 0.6429 (pm20) REVERT: H 60 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: E 56 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7832 (ttp) REVERT: E 124 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7156 (tt0) REVERT: E 132 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: E 294 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6363 (tmt) REVERT: E 322 ASP cc_start: 0.7958 (p0) cc_final: 0.7075 (t0) REVERT: E 430 TYR cc_start: 0.7383 (m-80) cc_final: 0.6486 (m-80) REVERT: E 474 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8258 (pptt) REVERT: E 490 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: E 553 MET cc_start: 0.7479 (mtp) cc_final: 0.7233 (mtp) REVERT: E 569 LEU cc_start: 0.8617 (tp) cc_final: 0.8408 (tp) REVERT: E 587 TYR cc_start: 0.7833 (m-80) cc_final: 0.7607 (m-80) REVERT: F 124 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7053 (mp0) REVERT: F 230 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.7133 (m-40) REVERT: F 294 MET cc_start: 0.7195 (tmt) cc_final: 0.6786 (tpt) REVERT: F 322 ASP cc_start: 0.8033 (p0) cc_final: 0.7052 (t0) REVERT: F 353 GLU cc_start: 0.7928 (mp0) cc_final: 0.7574 (pm20) REVERT: F 354 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7691 (mp) REVERT: F 430 TYR cc_start: 0.7170 (m-80) cc_final: 0.6337 (m-80) REVERT: F 474 LYS cc_start: 0.8241 (tptt) cc_final: 0.7992 (tptp) REVERT: F 483 ASP cc_start: 0.9320 (m-30) cc_final: 0.9013 (m-30) REVERT: F 541 ASN cc_start: 0.8656 (p0) cc_final: 0.8342 (p0) outliers start: 50 outliers final: 16 residues processed: 159 average time/residue: 0.4690 time to fit residues: 81.8522 Evaluate side-chains 135 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 275 HIS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 699 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN E 90 ASN E 275 HIS ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.162730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.128412 restraints weight = 21197.972| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 4.14 r_work: 0.3988 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11016 Z= 0.145 Angle : 0.737 18.731 14954 Z= 0.355 Chirality : 0.046 0.178 1648 Planarity : 0.004 0.029 1896 Dihedral : 7.611 59.138 1638 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.51 % Allowed : 19.82 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1274 helix: -0.25 (0.39), residues: 154 sheet: -1.39 (0.33), residues: 196 loop : -0.43 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 389 TYR 0.029 0.001 TYR E 507 PHE 0.012 0.002 PHE F 428 TRP 0.012 0.001 TRP F 133 HIS 0.019 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00340 (10970) covalent geometry : angle 0.70019 (14850) SS BOND : bond 0.00356 ( 34) SS BOND : angle 1.05150 ( 68) hydrogen bonds : bond 0.03951 ( 252) hydrogen bonds : angle 6.46492 ( 606) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 3.84826 ( 6) link_NAG-ASN : bond 0.00777 ( 8) link_NAG-ASN : angle 5.29910 ( 24) link_TRANS : bond 0.00057 ( 2) link_TRANS : angle 0.38970 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 VAL cc_start: 0.6145 (m) cc_final: 0.5920 (t) REVERT: C 4 GLN cc_start: 0.6897 (tp40) cc_final: 0.6486 (pm20) REVERT: E 56 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7698 (ttp) REVERT: E 132 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: E 177 GLN cc_start: 0.8240 (pp30) cc_final: 0.7754 (pp30) REVERT: E 294 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6438 (tmt) REVERT: E 318 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: E 322 ASP cc_start: 0.7927 (p0) cc_final: 0.7078 (t0) REVERT: E 430 TYR cc_start: 0.7377 (m-80) cc_final: 0.6468 (m-80) REVERT: E 474 LYS cc_start: 0.8719 (tmmt) cc_final: 0.8310 (pptt) REVERT: E 569 LEU cc_start: 0.8519 (tp) cc_final: 0.8281 (tp) REVERT: E 587 TYR cc_start: 0.7804 (m-80) cc_final: 0.7601 (m-80) REVERT: F 56 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7772 (ttp) REVERT: F 124 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7077 (mp0) REVERT: F 230 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6899 (m-40) REVERT: F 294 MET cc_start: 0.7193 (tmt) cc_final: 0.6860 (tpt) REVERT: F 322 ASP cc_start: 0.8028 (p0) cc_final: 0.7113 (t0) REVERT: F 353 GLU cc_start: 0.7920 (mp0) cc_final: 0.7580 (pm20) REVERT: F 354 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7635 (mp) REVERT: F 430 TYR cc_start: 0.7006 (m-80) cc_final: 0.6188 (m-80) REVERT: F 474 LYS cc_start: 0.8247 (tptt) cc_final: 0.7877 (tptt) REVERT: F 483 ASP cc_start: 0.9272 (m-30) cc_final: 0.8977 (m-30) REVERT: F 541 ASN cc_start: 0.8675 (p0) cc_final: 0.8346 (p0) outliers start: 42 outliers final: 16 residues processed: 157 average time/residue: 0.4548 time to fit residues: 78.8648 Evaluate side-chains 141 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 275 HIS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 715 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 105 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN E 275 HIS ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.162286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.127876 restraints weight = 21205.985| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 4.15 r_work: 0.3969 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11016 Z= 0.159 Angle : 0.734 18.549 14954 Z= 0.355 Chirality : 0.047 0.166 1648 Planarity : 0.004 0.029 1896 Dihedral : 7.559 58.734 1638 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.01 % Allowed : 20.82 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.24), residues: 1274 helix: -0.23 (0.40), residues: 154 sheet: -1.28 (0.34), residues: 186 loop : -0.44 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 389 TYR 0.025 0.001 TYR E 507 PHE 0.031 0.002 PHE F 256 TRP 0.012 0.001 TRP F 133 HIS 0.008 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00377 (10970) covalent geometry : angle 0.69794 (14850) SS BOND : bond 0.00362 ( 34) SS BOND : angle 0.99850 ( 68) hydrogen bonds : bond 0.03950 ( 252) hydrogen bonds : angle 6.36747 ( 606) link_BETA1-4 : bond 0.00409 ( 2) link_BETA1-4 : angle 3.92188 ( 6) link_NAG-ASN : bond 0.00763 ( 8) link_NAG-ASN : angle 5.23551 ( 24) link_TRANS : bond 0.00088 ( 2) link_TRANS : angle 0.36336 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.6864 (tp40) cc_final: 0.6436 (pm20) REVERT: C 29 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7545 (mptp) REVERT: H 65 ILE cc_start: 0.7709 (mm) cc_final: 0.7196 (tp) REVERT: E 56 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: E 124 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7166 (tt0) REVERT: E 132 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: E 275 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7362 (p90) REVERT: E 294 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6378 (tmt) REVERT: E 322 ASP cc_start: 0.7947 (p0) cc_final: 0.7106 (t0) REVERT: E 430 TYR cc_start: 0.7414 (m-80) cc_final: 0.6467 (m-80) REVERT: E 474 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8252 (pptt) REVERT: E 490 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: E 518 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5934 (m-80) REVERT: E 569 LEU cc_start: 0.8559 (tp) cc_final: 0.8306 (tp) REVERT: F 56 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: F 124 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7122 (mp0) REVERT: F 135 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7419 (tpm170) REVERT: F 294 MET cc_start: 0.7194 (tmt) cc_final: 0.6949 (tpt) REVERT: F 322 ASP cc_start: 0.8028 (p0) cc_final: 0.7103 (t0) REVERT: F 353 GLU cc_start: 0.7935 (mp0) cc_final: 0.7592 (pm20) REVERT: F 354 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7635 (mp) REVERT: F 430 TYR cc_start: 0.7098 (m-80) cc_final: 0.6277 (m-80) REVERT: F 483 ASP cc_start: 0.9253 (m-30) cc_final: 0.8950 (m-30) REVERT: F 541 ASN cc_start: 0.8701 (p0) cc_final: 0.8372 (p0) outliers start: 36 outliers final: 15 residues processed: 151 average time/residue: 0.4487 time to fit residues: 75.0022 Evaluate side-chains 148 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 699 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN E 275 HIS E 282 ASN F 275 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.162668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.128281 restraints weight = 21181.558| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 4.14 r_work: 0.3977 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11016 Z= 0.151 Angle : 0.734 18.321 14954 Z= 0.356 Chirality : 0.046 0.165 1648 Planarity : 0.004 0.029 1896 Dihedral : 7.506 58.641 1638 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.76 % Allowed : 21.24 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1274 helix: -0.20 (0.40), residues: 154 sheet: -1.40 (0.33), residues: 196 loop : -0.42 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 389 TYR 0.034 0.001 TYR E 587 PHE 0.013 0.002 PHE E 565 TRP 0.011 0.001 TRP F 133 HIS 0.008 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00357 (10970) covalent geometry : angle 0.69934 (14850) SS BOND : bond 0.00348 ( 34) SS BOND : angle 0.98948 ( 68) hydrogen bonds : bond 0.03861 ( 252) hydrogen bonds : angle 6.38719 ( 606) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 3.81509 ( 6) link_NAG-ASN : bond 0.00742 ( 8) link_NAG-ASN : angle 5.16950 ( 24) link_TRANS : bond 0.00091 ( 2) link_TRANS : angle 0.36746 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.6900 (tp40) cc_final: 0.6496 (pm20) REVERT: H 65 ILE cc_start: 0.7626 (mm) cc_final: 0.7131 (tp) REVERT: E 56 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7736 (ttp) REVERT: E 124 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7171 (tt0) REVERT: E 132 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: E 177 GLN cc_start: 0.8331 (pp30) cc_final: 0.7877 (pp30) REVERT: E 246 TYR cc_start: 0.8619 (m-80) cc_final: 0.8316 (t80) REVERT: E 322 ASP cc_start: 0.7985 (p0) cc_final: 0.7118 (t0) REVERT: E 430 TYR cc_start: 0.7419 (m-80) cc_final: 0.6462 (m-80) REVERT: E 474 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8248 (pptt) REVERT: E 518 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: E 569 LEU cc_start: 0.8633 (tp) cc_final: 0.8406 (tp) REVERT: F 56 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7709 (ttp) REVERT: F 124 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7115 (mp0) REVERT: F 322 ASP cc_start: 0.8036 (p0) cc_final: 0.7089 (t0) REVERT: F 353 GLU cc_start: 0.7960 (mp0) cc_final: 0.7606 (pm20) REVERT: F 354 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7618 (mp) REVERT: F 430 TYR cc_start: 0.7111 (m-80) cc_final: 0.6297 (m-80) REVERT: F 483 ASP cc_start: 0.9268 (m-30) cc_final: 0.8970 (m-30) REVERT: F 541 ASN cc_start: 0.8712 (p0) cc_final: 0.8377 (p0) outliers start: 33 outliers final: 17 residues processed: 152 average time/residue: 0.4345 time to fit residues: 73.2137 Evaluate side-chains 146 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 699 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN E 247 HIS E 264 HIS F 275 HIS ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.163069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.128587 restraints weight = 21152.579| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 4.15 r_work: 0.3979 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 11016 Z= 0.174 Angle : 0.787 18.205 14954 Z= 0.394 Chirality : 0.047 0.243 1648 Planarity : 0.005 0.118 1896 Dihedral : 7.502 58.495 1638 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.59 % Allowed : 21.49 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.24), residues: 1274 helix: -0.24 (0.39), residues: 154 sheet: -1.36 (0.34), residues: 196 loop : -0.40 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 389 TYR 0.044 0.002 TYR F 246 PHE 0.031 0.002 PHE E 256 TRP 0.011 0.001 TRP F 133 HIS 0.008 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00395 (10970) covalent geometry : angle 0.75461 (14850) SS BOND : bond 0.00299 ( 34) SS BOND : angle 1.04307 ( 68) hydrogen bonds : bond 0.03955 ( 252) hydrogen bonds : angle 6.40206 ( 606) link_BETA1-4 : bond 0.00239 ( 2) link_BETA1-4 : angle 3.79733 ( 6) link_NAG-ASN : bond 0.00754 ( 8) link_NAG-ASN : angle 5.14292 ( 24) link_TRANS : bond 0.00070 ( 2) link_TRANS : angle 0.38679 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.6902 (tp40) cc_final: 0.6469 (pm20) REVERT: C 29 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7593 (mptp) REVERT: H 65 ILE cc_start: 0.7623 (mm) cc_final: 0.7131 (tp) REVERT: E 56 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7724 (ttp) REVERT: E 124 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7061 (tt0) REVERT: E 132 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: E 177 GLN cc_start: 0.8313 (pp30) cc_final: 0.7853 (pp30) REVERT: E 294 MET cc_start: 0.6825 (tmm) cc_final: 0.6615 (tmt) REVERT: E 318 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6191 (tp30) REVERT: E 322 ASP cc_start: 0.7976 (p0) cc_final: 0.7122 (t0) REVERT: E 430 TYR cc_start: 0.7422 (m-80) cc_final: 0.6467 (m-80) REVERT: E 474 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8269 (pptt) REVERT: E 518 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: E 569 LEU cc_start: 0.8671 (tp) cc_final: 0.8463 (tp) REVERT: F 56 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: F 124 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7134 (mp0) REVERT: F 135 ARG cc_start: 0.7879 (mmt180) cc_final: 0.7410 (tpm170) REVERT: F 246 TYR cc_start: 0.8660 (m-80) cc_final: 0.8457 (m-80) REVERT: F 322 ASP cc_start: 0.8036 (p0) cc_final: 0.7091 (t0) REVERT: F 353 GLU cc_start: 0.7954 (mp0) cc_final: 0.7562 (pm20) REVERT: F 354 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7599 (mp) REVERT: F 430 TYR cc_start: 0.7088 (m-80) cc_final: 0.6269 (m-80) REVERT: F 483 ASP cc_start: 0.9264 (m-30) cc_final: 0.8958 (m-30) REVERT: F 541 ASN cc_start: 0.8723 (p0) cc_final: 0.8387 (p0) outliers start: 31 outliers final: 18 residues processed: 147 average time/residue: 0.4434 time to fit residues: 72.2412 Evaluate side-chains 147 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain G residue 69 TYR Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 512 TYR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 144 HIS Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 ILE Chi-restraints excluded: chain F residue 699 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 0.0370 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.163249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.129129 restraints weight = 21099.881| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 4.15 r_work: 0.3977 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11016 Z= 0.132 Angle : 0.753 17.954 14954 Z= 0.362 Chirality : 0.046 0.160 1648 Planarity : 0.004 0.029 1896 Dihedral : 7.297 58.300 1638 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.17 % Allowed : 22.07 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1274 helix: -0.10 (0.41), residues: 154 sheet: -1.28 (0.34), residues: 196 loop : -0.35 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 389 TYR 0.032 0.001 TYR E 507 PHE 0.012 0.001 PHE E 565 TRP 0.010 0.001 TRP F 133 HIS 0.009 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00306 (10970) covalent geometry : angle 0.72118 (14850) SS BOND : bond 0.00319 ( 34) SS BOND : angle 0.97066 ( 68) hydrogen bonds : bond 0.03727 ( 252) hydrogen bonds : angle 6.35648 ( 606) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 3.60301 ( 6) link_NAG-ASN : bond 0.00739 ( 8) link_NAG-ASN : angle 5.03744 ( 24) link_TRANS : bond 0.00048 ( 2) link_TRANS : angle 0.37400 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.65 seconds wall clock time: 75 minutes 14.60 seconds (4514.60 seconds total)