Starting phenix.real_space_refine on Wed Mar 4 14:16:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2t_34443/03_2026/8h2t_34443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2t_34443/03_2026/8h2t_34443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h2t_34443/03_2026/8h2t_34443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2t_34443/03_2026/8h2t_34443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h2t_34443/03_2026/8h2t_34443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2t_34443/03_2026/8h2t_34443.map" } resolution = 2.59 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 9 7.16 5 S 87 5.16 5 C 9066 2.51 5 N 2568 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 14370 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "A" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "D" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "G" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "H" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 681 SG CYS B 85 63.869 23.859 63.621 1.00 77.23 S ATOM 837 SG CYS B 106 64.771 24.572 60.097 1.00 86.23 S ATOM 5453 SG CYS D 85 92.651 68.268 63.635 1.00 82.70 S ATOM 5609 SG CYS D 106 91.640 68.795 60.069 1.00 84.01 S ATOM 10225 SG CYS G 85 39.814 71.048 63.604 1.00 79.87 S ATOM 10381 SG CYS G 106 39.938 69.893 60.076 1.00 85.39 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 230 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG B 230 " occ=0.51 residue: pdb=" N AARG D 230 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG D 230 " occ=0.51 residue: pdb=" N AARG G 230 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG G 230 " occ=0.54 Time building chain proxies: 5.27, per 1000 atoms: 0.37 Number of scatterers: 14370 At special positions: 0 Unit cell: (121.55, 120.7, 95.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 9 26.01 S 87 16.00 O 2640 8.00 N 2568 7.00 C 9066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 501 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 87 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 109 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 106 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 85 " pdb=" FES D 501 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 87 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 106 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 85 " pdb=" FES G 501 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 87 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 109 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 85 " Number of angles added : 9 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 37.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 7 through 13 Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.553A pdb=" N THR B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 37 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.976A pdb=" N PHE B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 221 through 233 removed outlier: 4.073A pdb=" N THR B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.687A pdb=" N PHE B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 352 through 368 removed outlier: 4.464A pdb=" N LEU B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.595A pdb=" N LYS B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.709A pdb=" N ARG B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 24 Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.589A pdb=" N ALA A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.626A pdb=" N LEU A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.632A pdb=" N GLN A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 13 Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.553A pdb=" N THR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 124 through 129 removed outlier: 4.255A pdb=" N GLU D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.970A pdb=" N PHE D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 221 through 233 removed outlier: 4.050A pdb=" N THR D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.786A pdb=" N PHE D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 297 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 352 through 368 removed outlier: 4.448A pdb=" N LEU D 356 " --> pdb=" O PRO D 352 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 388 Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.559A pdb=" N LYS D 408 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 436 removed outlier: 3.722A pdb=" N ARG D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 26 through 32 removed outlier: 3.570A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 73 removed outlier: 3.598A pdb=" N LEU E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.593A pdb=" N GLN E 81 " --> pdb=" O PHE E 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 13 Processing helix chain 'G' and resid 22 through 27 removed outlier: 3.552A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 50 through 52 No H-bonds generated for 'chain 'G' and resid 50 through 52' Processing helix chain 'G' and resid 124 through 129 removed outlier: 4.224A pdb=" N GLU G 129 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'G' and resid 174 through 183 Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.982A pdb=" N PHE G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 211 " --> pdb=" O PHE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 221 Processing helix chain 'G' and resid 221 through 233 removed outlier: 4.046A pdb=" N THR G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 249 Processing helix chain 'G' and resid 250 through 253 Processing helix chain 'G' and resid 254 through 262 removed outlier: 3.698A pdb=" N PHE G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY G 262 " --> pdb=" O PHE G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 297 Processing helix chain 'G' and resid 299 through 307 Processing helix chain 'G' and resid 352 through 368 removed outlier: 4.462A pdb=" N LEU G 356 " --> pdb=" O PRO G 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER G 368 " --> pdb=" O ARG G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 388 Processing helix chain 'G' and resid 403 through 409 removed outlier: 3.567A pdb=" N LYS G 408 " --> pdb=" O SER G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 436 removed outlier: 3.703A pdb=" N ARG G 423 " --> pdb=" O GLU G 419 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR G 436 " --> pdb=" O ARG G 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 24 Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.598A pdb=" N ALA H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 73 removed outlier: 3.641A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.604A pdb=" N GLN H 81 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 48 removed outlier: 5.776A pdb=" N TYR B 45 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 157 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 47 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.353A pdb=" N ASP B 57 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B 80 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.026A pdb=" N THR B 112 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.390A pdb=" N ARG B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 327 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 312 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.529A pdb=" N LEU A 58 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N THR A 35 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 140 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ASP A 37 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 142 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 39 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU A 148 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 131 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 144 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 129 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 146 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 148 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.529A pdb=" N LEU A 58 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N THR A 35 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 140 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ASP A 37 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 142 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 39 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU A 148 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 131 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 144 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 129 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 146 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 148 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 104 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 98 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 106 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB1, first strand: chain 'D' and resid 44 through 48 removed outlier: 5.795A pdb=" N TYR D 45 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 157 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY D 47 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.344A pdb=" N ASP D 57 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA D 80 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 103 through 105 removed outlier: 6.990A pdb=" N THR D 112 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 189 through 191 Processing sheet with id=AB5, first strand: chain 'D' and resid 189 through 191 removed outlier: 6.349A pdb=" N ARG D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 327 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 312 " --> pdb=" O THR D 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 56 through 60 removed outlier: 3.502A pdb=" N LEU E 58 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR E 35 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 142 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP E 37 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LYS E 144 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE E 39 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL E 146 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TRP E 41 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU E 148 " --> pdb=" O TRP E 41 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 131 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS E 144 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 129 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 146 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU E 148 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 125 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 56 through 60 removed outlier: 3.502A pdb=" N LEU E 58 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR E 35 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 142 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP E 37 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LYS E 144 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE E 39 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL E 146 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TRP E 41 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU E 148 " --> pdb=" O TRP E 41 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 131 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS E 144 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 129 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 146 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU E 148 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 125 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG E 104 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE E 98 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL E 106 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=AB9, first strand: chain 'G' and resid 44 through 48 removed outlier: 5.810A pdb=" N TYR G 45 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL G 157 " --> pdb=" O TYR G 45 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY G 47 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 97 through 99 removed outlier: 4.361A pdb=" N ASP G 57 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA G 80 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 103 through 105 removed outlier: 7.016A pdb=" N THR G 112 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 189 through 191 Processing sheet with id=AC4, first strand: chain 'G' and resid 189 through 191 removed outlier: 6.366A pdb=" N ARG G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 327 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN G 312 " --> pdb=" O THR G 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.568A pdb=" N LEU H 58 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR H 35 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ARG H 140 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N ASP H 37 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR H 142 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 39 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 148 " --> pdb=" O PRO H 43 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS H 131 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS H 144 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE H 129 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 146 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR H 127 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU H 148 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 125 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.568A pdb=" N LEU H 58 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR H 35 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ARG H 140 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N ASP H 37 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR H 142 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 39 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 148 " --> pdb=" O PRO H 43 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS H 131 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS H 144 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE H 129 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 146 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR H 127 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU H 148 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 125 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG H 104 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE H 98 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL H 106 " --> pdb=" O GLU H 96 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 6505 1.42 - 1.62: 8099 1.62 - 1.81: 137 1.81 - 2.01: 1 2.01 - 2.20: 12 Bond restraints: 14754 Sorted by residual: bond pdb=" N IAC B 502 " pdb=" C IAC B 502 " ideal model delta sigma weight residual 1.363 1.331 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" N IAC D 502 " pdb=" C IAC D 502 " ideal model delta sigma weight residual 1.363 1.331 0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C7 IAC B 502 " pdb=" C8 IAC B 502 " ideal model delta sigma weight residual 1.366 1.397 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N IAC G 502 " pdb=" C IAC G 502 " ideal model delta sigma weight residual 1.363 1.332 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C7 IAC D 502 " pdb=" C8 IAC D 502 " ideal model delta sigma weight residual 1.366 1.396 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 14749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 19776 2.42 - 4.84: 194 4.84 - 7.27: 19 7.27 - 9.69: 2 9.69 - 12.11: 1 Bond angle restraints: 19992 Sorted by residual: angle pdb=" CB MET D 215 " pdb=" CG MET D 215 " pdb=" SD MET D 215 " ideal model delta sigma weight residual 112.70 124.81 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" N ILE G 325 " pdb=" CA ILE G 325 " pdb=" C ILE G 325 " ideal model delta sigma weight residual 113.42 108.99 4.43 1.17e+00 7.31e-01 1.44e+01 angle pdb=" N ILE B 325 " pdb=" CA ILE B 325 " pdb=" C ILE B 325 " ideal model delta sigma weight residual 113.42 108.99 4.43 1.17e+00 7.31e-01 1.43e+01 angle pdb=" N ILE D 325 " pdb=" CA ILE D 325 " pdb=" C ILE D 325 " ideal model delta sigma weight residual 113.42 109.04 4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" C HIS B 276 " pdb=" N PHE B 277 " pdb=" CA PHE B 277 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 ... (remaining 19987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 7529 16.96 - 33.91: 892 33.91 - 50.87: 235 50.87 - 67.82: 57 67.82 - 84.78: 23 Dihedral angle restraints: 8736 sinusoidal: 3567 harmonic: 5169 Sorted by residual: dihedral pdb=" CA LEU E 90 " pdb=" C LEU E 90 " pdb=" N GLN E 91 " pdb=" CA GLN E 91 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU A 90 " pdb=" C LEU A 90 " pdb=" N GLN A 91 " pdb=" CA GLN A 91 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU H 90 " pdb=" C LEU H 90 " pdb=" N GLN H 91 " pdb=" CA GLN H 91 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1254 0.030 - 0.060: 527 0.060 - 0.091: 174 0.091 - 0.121: 108 0.121 - 0.151: 19 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA HIS D 216 " pdb=" N HIS D 216 " pdb=" C HIS D 216 " pdb=" CB HIS D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE G 263 " pdb=" N ILE G 263 " pdb=" C ILE G 263 " pdb=" CB ILE G 263 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA HIS B 216 " pdb=" N HIS B 216 " pdb=" C HIS B 216 " pdb=" CB HIS B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2079 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 101 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" CD GLU E 101 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU E 101 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU E 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 277 " -0.011 2.00e-02 2.50e+03 1.73e-02 5.23e+00 pdb=" CG PHE B 277 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 277 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 277 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 277 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 277 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 277 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 101 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" CD GLU H 101 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 101 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 101 " -0.012 2.00e-02 2.50e+03 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 178 2.61 - 3.19: 11598 3.19 - 3.76: 22021 3.76 - 4.33: 32163 4.33 - 4.90: 53779 Nonbonded interactions: 119739 Sorted by model distance: nonbonded pdb=" OD2 ASP B 377 " pdb="FE FE B 503 " model vdw 2.043 2.260 nonbonded pdb=" OD2 ASP D 377 " pdb="FE FE D 503 " model vdw 2.043 2.260 nonbonded pdb=" OD2 ASP G 377 " pdb="FE FE G 503 " model vdw 2.043 2.260 nonbonded pdb=" OD1 ASP G 377 " pdb="FE FE G 503 " model vdw 2.055 2.260 nonbonded pdb=" OD1 ASP B 377 " pdb="FE FE B 503 " model vdw 2.058 2.260 ... (remaining 119734 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 3 through 229 or resid 231 through 503)) selection = (chain 'D' and (resid 3 through 229 or resid 231 through 503)) selection = (chain 'G' and (resid 3 through 229 or resid 231 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.640 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 0.044 14766 Z= 0.145 Angle : 0.597 12.109 20001 Z= 0.320 Chirality : 0.043 0.151 2082 Planarity : 0.005 0.043 2634 Dihedral : 16.316 84.781 5412 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 21.54 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.43 (0.20), residues: 1773 helix: 0.78 (0.23), residues: 549 sheet: 0.66 (0.29), residues: 309 loop : -0.05 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 146 TYR 0.013 0.001 TYR G 426 PHE 0.039 0.001 PHE B 277 TRP 0.021 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00318 (14754) covalent geometry : angle 0.58831 (19992) hydrogen bonds : bond 0.12186 ( 629) hydrogen bonds : angle 6.17027 ( 1944) metal coordination : bond 0.00705 ( 12) metal coordination : angle 4.78625 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.593 Fit side-chains REVERT: B 437 MET cc_start: 0.7673 (mmt) cc_final: 0.7446 (mmt) REVERT: D 209 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: D 255 TYR cc_start: 0.8111 (m-10) cc_final: 0.7725 (m-10) outliers start: 23 outliers final: 21 residues processed: 188 average time/residue: 0.7138 time to fit residues: 144.9851 Evaluate side-chains 184 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 436 THR Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090040 restraints weight = 39216.139| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.98 r_work: 0.3189 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14766 Z= 0.110 Angle : 0.528 8.242 20001 Z= 0.278 Chirality : 0.042 0.140 2082 Planarity : 0.004 0.044 2634 Dihedral : 5.747 57.986 2028 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.31 % Allowed : 19.83 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.73 (0.20), residues: 1773 helix: 1.17 (0.23), residues: 552 sheet: 0.35 (0.28), residues: 336 loop : 0.23 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 146 TYR 0.009 0.001 TYR D 426 PHE 0.031 0.001 PHE B 277 TRP 0.020 0.001 TRP D 429 HIS 0.003 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00240 (14754) covalent geometry : angle 0.51818 (19992) hydrogen bonds : bond 0.03900 ( 629) hydrogen bonds : angle 4.61102 ( 1944) metal coordination : bond 0.00637 ( 12) metal coordination : angle 4.80691 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.560 Fit side-chains REVERT: B 308 MET cc_start: 0.6899 (mtp) cc_final: 0.6693 (ttt) REVERT: B 437 MET cc_start: 0.7788 (mmt) cc_final: 0.7472 (mmt) REVERT: E 29 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8233 (mt-10) REVERT: E 96 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8119 (mt-10) REVERT: G 19 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7601 (ptt-90) REVERT: G 338 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7639 (ttt-90) REVERT: G 422 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7347 (mpt) outliers start: 35 outliers final: 4 residues processed: 201 average time/residue: 0.7217 time to fit residues: 156.4923 Evaluate side-chains 174 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.081686 restraints weight = 52789.888| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.59 r_work: 0.2838 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14766 Z= 0.193 Angle : 0.589 10.533 20001 Z= 0.310 Chirality : 0.045 0.159 2082 Planarity : 0.005 0.050 2634 Dihedral : 4.864 41.526 1993 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 2.24 % Allowed : 20.03 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.61 (0.20), residues: 1773 helix: 1.05 (0.23), residues: 552 sheet: 0.47 (0.29), residues: 306 loop : 0.09 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 146 TYR 0.011 0.002 TYR B 45 PHE 0.032 0.002 PHE B 277 TRP 0.018 0.002 TRP D 429 HIS 0.005 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00456 (14754) covalent geometry : angle 0.57989 (19992) hydrogen bonds : bond 0.04871 ( 629) hydrogen bonds : angle 4.80906 ( 1944) metal coordination : bond 0.01806 ( 12) metal coordination : angle 4.79283 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.593 Fit side-chains REVERT: B 338 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7947 (ttt-90) REVERT: B 422 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: B 437 MET cc_start: 0.7709 (mmt) cc_final: 0.7473 (mmt) REVERT: A 120 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: D 52 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8436 (pp) REVERT: D 209 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: E 29 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8166 (mt-10) REVERT: E 96 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8098 (mt-10) REVERT: G 19 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7439 (ptt-90) REVERT: G 338 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7529 (ttt-90) REVERT: G 422 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6232 (mmt) outliers start: 34 outliers final: 11 residues processed: 186 average time/residue: 0.7630 time to fit residues: 152.9292 Evaluate side-chains 182 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.080241 restraints weight = 48871.346| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.45 r_work: 0.2813 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14766 Z= 0.269 Angle : 0.640 10.961 20001 Z= 0.339 Chirality : 0.048 0.178 2082 Planarity : 0.005 0.050 2634 Dihedral : 5.127 44.172 1992 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.92 % Rotamer: Outliers : 2.57 % Allowed : 19.63 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.41 (0.20), residues: 1773 helix: 0.89 (0.23), residues: 552 sheet: 0.46 (0.29), residues: 306 loop : -0.08 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 146 TYR 0.013 0.002 TYR B 45 PHE 0.035 0.002 PHE B 277 TRP 0.019 0.002 TRP D 429 HIS 0.006 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00646 (14754) covalent geometry : angle 0.63218 (19992) hydrogen bonds : bond 0.05600 ( 629) hydrogen bonds : angle 5.04550 ( 1944) metal coordination : bond 0.02595 ( 12) metal coordination : angle 4.67790 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.568 Fit side-chains REVERT: B 180 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: B 308 MET cc_start: 0.7228 (mtp) cc_final: 0.6961 (ttt) REVERT: B 338 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7921 (ttt-90) REVERT: B 422 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7079 (mmt) REVERT: B 437 MET cc_start: 0.7585 (mmt) cc_final: 0.7330 (mmt) REVERT: A 120 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8248 (mm-30) REVERT: D 52 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8461 (pp) REVERT: D 209 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: D 437 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6766 (mmm) REVERT: G 19 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7431 (ptt-90) REVERT: G 338 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7568 (ttt-90) REVERT: G 422 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6255 (mmt) outliers start: 39 outliers final: 13 residues processed: 187 average time/residue: 0.7679 time to fit residues: 154.5311 Evaluate side-chains 183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083713 restraints weight = 43741.799| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.32 r_work: 0.2876 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14766 Z= 0.134 Angle : 0.553 10.722 20001 Z= 0.291 Chirality : 0.043 0.171 2082 Planarity : 0.004 0.047 2634 Dihedral : 4.799 46.306 1992 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.37 % Rotamer: Outliers : 2.24 % Allowed : 20.42 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.57 (0.20), residues: 1773 helix: 1.10 (0.23), residues: 555 sheet: 0.27 (0.28), residues: 336 loop : 0.07 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 146 TYR 0.009 0.001 TYR B 45 PHE 0.034 0.001 PHE B 277 TRP 0.018 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00309 (14754) covalent geometry : angle 0.54511 (19992) hydrogen bonds : bond 0.04128 ( 629) hydrogen bonds : angle 4.56823 ( 1944) metal coordination : bond 0.01129 ( 12) metal coordination : angle 4.49079 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.552 Fit side-chains REVERT: B 180 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8119 (ttp) REVERT: B 338 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7860 (ttt-90) REVERT: B 437 MET cc_start: 0.7673 (mmt) cc_final: 0.7431 (mmt) REVERT: A 120 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: D 437 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6531 (mmm) REVERT: E 29 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8130 (mt-10) REVERT: G 19 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7472 (ptt-90) REVERT: G 34 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7063 (pt0) REVERT: G 338 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7537 (ttt-90) REVERT: G 422 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6107 (mmt) outliers start: 34 outliers final: 12 residues processed: 192 average time/residue: 0.6876 time to fit residues: 142.6312 Evaluate side-chains 182 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 32 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 166 optimal weight: 0.0030 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083337 restraints weight = 55825.361| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.68 r_work: 0.2853 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14766 Z= 0.141 Angle : 0.563 11.219 20001 Z= 0.292 Chirality : 0.043 0.149 2082 Planarity : 0.004 0.048 2634 Dihedral : 4.756 45.737 1992 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 2.04 % Allowed : 20.82 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.70 (0.20), residues: 1773 helix: 1.16 (0.23), residues: 555 sheet: 0.46 (0.29), residues: 306 loop : 0.15 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.010 0.001 TYR B 45 PHE 0.032 0.001 PHE B 277 TRP 0.021 0.001 TRP D 429 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00327 (14754) covalent geometry : angle 0.55477 (19992) hydrogen bonds : bond 0.04196 ( 629) hydrogen bonds : angle 4.53739 ( 1944) metal coordination : bond 0.01185 ( 12) metal coordination : angle 4.62094 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.471 Fit side-chains REVERT: B 180 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8163 (ttp) REVERT: B 338 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7908 (ttt-90) REVERT: B 437 MET cc_start: 0.7663 (mmt) cc_final: 0.7399 (mmt) REVERT: A 120 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: D 210 ASN cc_start: 0.8674 (t0) cc_final: 0.8368 (t0) REVERT: G 19 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7476 (ptt-90) REVERT: G 34 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7103 (pt0) REVERT: G 338 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7545 (ttt-90) REVERT: G 422 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.5976 (mmt) REVERT: H 49 GLU cc_start: 0.8251 (tp30) cc_final: 0.7982 (tp30) outliers start: 31 outliers final: 11 residues processed: 186 average time/residue: 0.7120 time to fit residues: 142.6443 Evaluate side-chains 182 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 137 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083439 restraints weight = 43290.752| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.30 r_work: 0.2867 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14766 Z= 0.157 Angle : 0.578 11.992 20001 Z= 0.301 Chirality : 0.044 0.156 2082 Planarity : 0.004 0.048 2634 Dihedral : 4.799 45.863 1992 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 20.82 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.67 (0.20), residues: 1773 helix: 1.13 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.12 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.013 0.001 TYR B 426 PHE 0.031 0.002 PHE B 277 TRP 0.019 0.001 TRP D 429 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00369 (14754) covalent geometry : angle 0.56976 (19992) hydrogen bonds : bond 0.04377 ( 629) hydrogen bonds : angle 4.58826 ( 1944) metal coordination : bond 0.01358 ( 12) metal coordination : angle 4.65248 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.430 Fit side-chains REVERT: B 180 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8139 (ttp) REVERT: B 338 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7905 (ttt-90) REVERT: B 437 MET cc_start: 0.7671 (mmt) cc_final: 0.7404 (mmt) REVERT: A 104 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7179 (mtm110) REVERT: A 120 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (mm-30) REVERT: G 19 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7463 (ptt-90) REVERT: G 34 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7046 (pt0) REVERT: G 338 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7534 (ttt-90) REVERT: G 422 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6139 (mmt) REVERT: H 49 GLU cc_start: 0.8265 (tp30) cc_final: 0.7971 (tp30) outliers start: 32 outliers final: 17 residues processed: 181 average time/residue: 0.7491 time to fit residues: 146.3298 Evaluate side-chains 188 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 57 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 157 optimal weight: 0.0070 chunk 133 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.083478 restraints weight = 52519.084| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.59 r_work: 0.2861 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14766 Z= 0.143 Angle : 0.568 10.879 20001 Z= 0.295 Chirality : 0.043 0.150 2082 Planarity : 0.004 0.047 2634 Dihedral : 4.751 46.225 1992 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 1.91 % Allowed : 20.95 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.71 (0.20), residues: 1773 helix: 1.17 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.16 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 146 TYR 0.010 0.001 TYR D 426 PHE 0.035 0.001 PHE B 277 TRP 0.020 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00333 (14754) covalent geometry : angle 0.55923 (19992) hydrogen bonds : bond 0.04179 ( 629) hydrogen bonds : angle 4.51389 ( 1944) metal coordination : bond 0.01181 ( 12) metal coordination : angle 4.63918 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.575 Fit side-chains REVERT: B 180 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8139 (ttp) REVERT: B 255 TYR cc_start: 0.8249 (m-80) cc_final: 0.7501 (m-80) REVERT: B 338 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7917 (ttt-90) REVERT: B 422 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7056 (mmt) REVERT: B 437 MET cc_start: 0.7660 (mmt) cc_final: 0.7417 (mmt) REVERT: A 104 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7163 (mtm110) REVERT: A 120 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: D 210 ASN cc_start: 0.8621 (t0) cc_final: 0.8303 (t0) REVERT: D 426 TYR cc_start: 0.8288 (m-80) cc_final: 0.7944 (m-80) REVERT: G 19 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7488 (ptt-90) REVERT: G 34 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7068 (pt0) REVERT: G 338 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7545 (ttt-90) REVERT: G 422 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6089 (mmt) REVERT: H 49 GLU cc_start: 0.8316 (tp30) cc_final: 0.8007 (tp30) outliers start: 29 outliers final: 17 residues processed: 185 average time/residue: 0.7612 time to fit residues: 151.9486 Evaluate side-chains 190 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083813 restraints weight = 45882.327| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.38 r_work: 0.2871 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14766 Z= 0.146 Angle : 0.576 12.629 20001 Z= 0.300 Chirality : 0.044 0.153 2082 Planarity : 0.004 0.048 2634 Dihedral : 4.756 46.190 1992 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 1.84 % Allowed : 21.21 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.70 (0.20), residues: 1773 helix: 1.16 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.15 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 146 TYR 0.010 0.001 TYR B 45 PHE 0.034 0.001 PHE B 277 TRP 0.023 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00343 (14754) covalent geometry : angle 0.56765 (19992) hydrogen bonds : bond 0.04207 ( 629) hydrogen bonds : angle 4.52512 ( 1944) metal coordination : bond 0.01211 ( 12) metal coordination : angle 4.66345 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.537 Fit side-chains REVERT: B 180 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8136 (ttp) REVERT: B 338 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7907 (ttt-90) REVERT: B 422 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7021 (mmt) REVERT: B 437 MET cc_start: 0.7670 (mmt) cc_final: 0.7428 (mmt) REVERT: A 104 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7171 (mtm110) REVERT: A 120 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: D 210 ASN cc_start: 0.8616 (t0) cc_final: 0.8292 (t0) REVERT: D 426 TYR cc_start: 0.8254 (m-80) cc_final: 0.7952 (m-80) REVERT: D 437 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6426 (mmm) REVERT: G 19 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7467 (ptt-90) REVERT: G 34 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7056 (pt0) REVERT: G 338 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7533 (ttt-90) REVERT: G 422 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6176 (mmt) REVERT: H 49 GLU cc_start: 0.8288 (tp30) cc_final: 0.7986 (tp30) outliers start: 28 outliers final: 16 residues processed: 178 average time/residue: 0.7759 time to fit residues: 148.6207 Evaluate side-chains 191 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 81 optimal weight: 0.0050 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084621 restraints weight = 54578.869| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.66 r_work: 0.2879 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14766 Z= 0.120 Angle : 0.554 12.199 20001 Z= 0.288 Chirality : 0.043 0.149 2082 Planarity : 0.004 0.046 2634 Dihedral : 4.654 45.848 1992 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 1.52 % Allowed : 21.34 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.80 (0.20), residues: 1773 helix: 1.25 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.23 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 146 TYR 0.012 0.001 TYR G 426 PHE 0.032 0.001 PHE B 277 TRP 0.023 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00275 (14754) covalent geometry : angle 0.54532 (19992) hydrogen bonds : bond 0.03839 ( 629) hydrogen bonds : angle 4.38497 ( 1944) metal coordination : bond 0.00817 ( 12) metal coordination : angle 4.67513 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.502 Fit side-chains REVERT: B 180 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8108 (ttp) REVERT: B 338 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7875 (ttt-90) REVERT: B 422 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7101 (mmt) REVERT: B 437 MET cc_start: 0.7678 (mmt) cc_final: 0.7391 (mmt) REVERT: A 120 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: D 210 ASN cc_start: 0.8586 (t0) cc_final: 0.8243 (t0) REVERT: D 426 TYR cc_start: 0.8268 (m-80) cc_final: 0.7915 (m-80) REVERT: D 437 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6369 (mmm) REVERT: G 338 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7524 (ttt-90) REVERT: G 422 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6031 (mmt) REVERT: G 426 TYR cc_start: 0.8160 (m-80) cc_final: 0.7946 (m-80) REVERT: H 49 GLU cc_start: 0.8301 (tp30) cc_final: 0.7993 (tp30) outliers start: 23 outliers final: 12 residues processed: 183 average time/residue: 0.7350 time to fit residues: 144.9227 Evaluate side-chains 183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.081592 restraints weight = 56519.142| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.69 r_work: 0.2827 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14766 Z= 0.212 Angle : 0.629 13.871 20001 Z= 0.328 Chirality : 0.046 0.185 2082 Planarity : 0.005 0.048 2634 Dihedral : 4.911 45.699 1992 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 1.25 % Allowed : 21.81 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.60 (0.20), residues: 1773 helix: 1.07 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.07 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 146 TYR 0.011 0.002 TYR G 25 PHE 0.032 0.002 PHE B 277 TRP 0.026 0.002 TRP D 429 HIS 0.006 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00509 (14754) covalent geometry : angle 0.62162 (19992) hydrogen bonds : bond 0.04922 ( 629) hydrogen bonds : angle 4.75360 ( 1944) metal coordination : bond 0.01975 ( 12) metal coordination : angle 4.63132 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.23 seconds wall clock time: 80 minutes 12.64 seconds (4812.64 seconds total)