Starting phenix.real_space_refine on Fri Jul 3 12:45:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h2t_34443/07_2026/8h2t_34443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2t_34443/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8h2t_34443/07_2026/8h2t_34443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h2t_34443/07_2026/8h2t_34443.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h2t_34443/07_2026/8h2t_34443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2t_34443/07_2026/8h2t_34443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h2t_34443/07_2026/8h2t_34443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2t_34443/07_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-6108/lib/python3.11/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: 4.56, per 1000 atoms: 0.32 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: 1.04 Conformation dependent library (CDL) restraints added in 725.0 milliseconds 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: 0.48 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: 2.50 Time building geometry restraints manager: 1.35 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: 1.130 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.880 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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/Z covalent geometry : bond 0.00318 / 0.14 (14754) covalent geometry : angle 0.58831 / 0.32 (19992) hydrogen bonds : bond 0.12186 / 8.14 ( 629) hydrogen bonds : angle 6.17027 / 4.19 ( 1944) metal coordination : bond 0.00705 / 0.45 ( 12) metal coordination : angle 4.78625 / 2.58 ( 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 : 0.553 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: 0.6510 time to fit residues: 132.7843 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 : 0.496 ------------------------------------------------------------------------------- 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... 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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/Z covalent geometry : bond 0.00240 / 0.11 (14754) covalent geometry : angle 0.51818 / 0.28 (19992) hydrogen bonds : bond 0.03900 / 2.57 ( 629) hydrogen bonds : angle 4.61102 / 3.18 ( 1944) metal coordination : bond 0.00637 / 0.41 ( 12) metal coordination : angle 4.80691 / 2.60 ( 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 : 0.587 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: 0.7353 time to fit residues: 159.7011 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 : 0.550 ------------------------------------------------------------------------------- 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: 0.9990 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: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3341 r_free = 0.3341 target = 0.104674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.082770 restraints weight = 53188.106| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.60 r_work: 0.2855 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14766 Z= 0.157 Angle : 0.562 10.084 20001 Z= 0.295 Chirality : 0.044 0.152 2082 Planarity : 0.004 0.050 2634 Dihedral : 4.729 40.368 1993 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 2.37 % Allowed : 19.76 % 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: 0.70 (0.20), residues: 1773 helix: 1.14 (0.23), residues: 552 sheet: 0.47 (0.29), residues: 306 loop : 0.16 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 146 TYR 0.010 0.001 TYR B 45 PHE 0.031 0.002 PHE B 277 TRP 0.018 0.001 TRP D 429 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (14754) covalent geometry : angle 0.55286 / 0.29 (19992) hydrogen bonds : bond 0.04457 / 2.93 ( 629) hydrogen bonds : angle 4.66822 / 3.23 ( 1944) metal coordination : bond 0.01369 / 0.87 ( 12) metal coordination : angle 4.81543 / 2.60 ( 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 205 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.613 Fit side-chains REVERT: B 338 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7930 (ttt-90) REVERT: B 422 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6979 (mmt) REVERT: A 120 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: D 52 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8433 (pp) REVERT: E 29 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8169 (mt-10) REVERT: E 96 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8084 (mt-10) REVERT: G 19 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7462 (ptt-90) REVERT: G 338 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7529 (ttt-90) outliers start: 36 outliers final: 12 residues processed: 189 average time/residue: 0.7502 time to fit residues: 153.4874 Evaluate side-chains 183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER 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 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 263 ILE Chi-restraints excluded: chain D residue 320 THR 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 275 VAL Chi-restraints excluded: chain G residue 338 ARG 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: 3.9990 chunk 58 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3312 r_free = 0.3312 target = 0.102785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.080933 restraints weight = 50336.653| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.50 r_work: 0.2822 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14766 Z= 0.230 Angle : 0.615 11.502 20001 Z= 0.324 Chirality : 0.046 0.171 2082 Planarity : 0.005 0.050 2634 Dihedral : 5.009 43.718 1992 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 2.31 % Allowed : 20.09 % Favored : 77.60 % 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: 0.52 (0.20), residues: 1773 helix: 1.00 (0.23), residues: 552 sheet: 0.45 (0.29), residues: 306 loop : 0.00 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 146 TYR 0.017 0.002 TYR B 426 PHE 0.033 0.002 PHE B 277 TRP 0.017 0.002 TRP D 429 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (14754) covalent geometry : angle 0.60704 / 0.32 (19992) hydrogen bonds : bond 0.05231 / 3.43 ( 629) hydrogen bonds : angle 4.91489 / 3.40 ( 1944) metal coordination : bond 0.02189 / 1.38 ( 12) metal coordination : angle 4.79064 / 2.58 ( 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 199 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.575 Fit side-chains REVERT: B 308 MET cc_start: 0.7179 (mtp) cc_final: 0.6896 (ttt) REVERT: B 338 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7910 (ttt-90) REVERT: B 422 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: A 120 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: D 52 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8450 (pp) REVERT: D 437 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6663 (mmm) REVERT: G 19 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7448 (ptt-90) REVERT: G 338 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7554 (ttt-90) REVERT: H 49 GLU cc_start: 0.8269 (tp30) cc_final: 0.7998 (tp30) outliers start: 35 outliers final: 12 residues processed: 184 average time/residue: 0.7571 time to fit residues: 150.7677 Evaluate side-chains 176 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 171 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3348 r_free = 0.3348 target = 0.105001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083653 restraints weight = 44088.263| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.32 r_work: 0.2873 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 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 = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14766 Z= 0.135 Angle : 0.550 10.755 20001 Z= 0.288 Chirality : 0.043 0.162 2082 Planarity : 0.004 0.048 2634 Dihedral : 4.767 45.358 1992 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.37 % Rotamer: Outliers : 1.91 % Allowed : 20.82 % Favored : 77.27 % 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: 0.68 (0.20), residues: 1773 helix: 1.13 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.14 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 146 TYR 0.010 0.001 TYR B 45 PHE 0.034 0.001 PHE B 277 TRP 0.017 0.001 TRP D 429 HIS 0.004 0.001 HIS E 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14754) covalent geometry : angle 0.54119 / 0.29 (19992) hydrogen bonds : bond 0.04131 / 2.72 ( 629) hydrogen bonds : angle 4.55733 / 3.16 ( 1944) metal coordination : bond 0.01102 / 0.70 ( 12) metal coordination : angle 4.60764 / 2.49 ( 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 200 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.631 Fit side-chains REVERT: B 338 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7857 (ttt-90) REVERT: B 422 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7033 (mmt) REVERT: B 437 MET cc_start: 0.7568 (mmt) cc_final: 0.7286 (mmt) REVERT: A 120 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: E 29 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8146 (mt-10) REVERT: G 19 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7474 (ptt-90) REVERT: G 34 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6942 (pt0) REVERT: G 338 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7538 (ttt-90) REVERT: H 49 GLU cc_start: 0.8271 (tp30) cc_final: 0.7965 (tp30) outliers start: 29 outliers final: 10 residues processed: 187 average time/residue: 0.7176 time to fit residues: 145.3031 Evaluate side-chains 177 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 263 ILE Chi-restraints excluded: chain E residue 116 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 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: 8.9990 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3369 r_free = 0.3369 target = 0.106360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.084542 restraints weight = 56892.895| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.70 r_work: 0.2880 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 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 = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14766 Z= 0.114 Angle : 0.538 11.107 20001 Z= 0.278 Chirality : 0.042 0.144 2082 Planarity : 0.004 0.047 2634 Dihedral : 4.595 44.422 1992 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.40 % Favored : 96.43 % Rotamer: Outliers : 1.71 % Allowed : 21.21 % 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: 0.80 (0.20), residues: 1773 helix: 1.28 (0.23), residues: 555 sheet: 0.42 (0.29), residues: 309 loop : 0.23 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 146 TYR 0.009 0.001 TYR B 45 PHE 0.031 0.001 PHE B 277 TRP 0.021 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (14754) covalent geometry : angle 0.52904 / 0.28 (19992) hydrogen bonds : bond 0.03750 / 2.47 ( 629) hydrogen bonds : angle 4.36109 / 3.03 ( 1944) metal coordination : bond 0.00829 / 0.53 ( 12) metal coordination : angle 4.68768 / 2.54 ( 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 203 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.584 Fit side-chains REVERT: B 180 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8226 (ttp) REVERT: B 338 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7865 (ttt-90) REVERT: B 437 MET cc_start: 0.7591 (mmt) cc_final: 0.7267 (mmt) REVERT: A 120 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: D 210 ASN cc_start: 0.8617 (t0) cc_final: 0.8335 (t0) REVERT: G 19 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7466 (ptt-90) REVERT: G 338 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7531 (ttt-90) REVERT: H 49 GLU cc_start: 0.8324 (tp30) cc_final: 0.7990 (tp30) outliers start: 26 outliers final: 10 residues processed: 191 average time/residue: 0.7019 time to fit residues: 145.3680 Evaluate side-chains 182 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 320 THR 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 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG 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: 10.0000 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3329 r_free = 0.3329 target = 0.103963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082408 restraints weight = 43396.320| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.29 r_work: 0.2852 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 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 = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14766 Z= 0.190 Angle : 0.599 13.092 20001 Z= 0.312 Chirality : 0.045 0.164 2082 Planarity : 0.005 0.048 2634 Dihedral : 4.869 45.755 1992 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 1.98 % Allowed : 20.88 % 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: 0.67 (0.20), residues: 1773 helix: 1.13 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.13 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.011 0.002 TYR B 45 PHE 0.031 0.002 PHE B 277 TRP 0.024 0.002 TRP D 429 HIS 0.005 0.001 HIS G 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (14754) covalent geometry : angle 0.59033 / 0.31 (19992) hydrogen bonds : bond 0.04748 / 3.12 ( 629) hydrogen bonds : angle 4.70884 / 3.26 ( 1944) metal coordination : bond 0.01760 / 1.11 ( 12) metal coordination : angle 4.77448 / 2.58 ( 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 197 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.556 Fit side-chains REVERT: B 180 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: B 338 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7911 (ttt-90) REVERT: B 437 MET cc_start: 0.7584 (mmt) cc_final: 0.7348 (mmt) REVERT: A 120 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8281 (mm-30) REVERT: D 437 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6587 (mmm) REVERT: G 19 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7441 (ptt-90) REVERT: G 338 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7527 (ttt-90) REVERT: H 49 GLU cc_start: 0.8346 (tp30) cc_final: 0.8021 (tp30) REVERT: H 96 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7342 (mt-10) outliers start: 30 outliers final: 14 residues processed: 184 average time/residue: 0.7312 time to fit residues: 145.1963 Evaluate side-chains 186 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 407 LEU 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 437 MET Chi-restraints excluded: chain E residue 114 THR 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 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain H residue 96 GLU 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: 8.9990 chunk 165 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 157 optimal weight: 0.0370 chunk 133 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3368 r_free = 0.3368 target = 0.106410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.084589 restraints weight = 52604.022| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.60 r_work: 0.2884 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 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 = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14766 Z= 0.119 Angle : 0.545 11.592 20001 Z= 0.284 Chirality : 0.043 0.165 2082 Planarity : 0.004 0.047 2634 Dihedral : 4.632 45.799 1992 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.37 % Rotamer: Outliers : 1.38 % Allowed : 21.67 % 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: 0.81 (0.20), residues: 1773 helix: 1.27 (0.23), residues: 555 sheet: 0.39 (0.29), residues: 309 loop : 0.26 (0.21), residues: 909 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 0.035 0.001 PHE B 277 TRP 0.025 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14754) covalent geometry : angle 0.53653 / 0.28 (19992) hydrogen bonds : bond 0.03798 / 2.50 ( 629) hydrogen bonds : angle 4.37283 / 3.04 ( 1944) metal coordination : bond 0.00849 / 0.54 ( 12) metal coordination : angle 4.59276 / 2.48 ( 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 194 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.545 Fit side-chains REVERT: B 180 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8196 (ttp) REVERT: B 338 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7864 (ttt-90) REVERT: B 437 MET cc_start: 0.7565 (mmt) cc_final: 0.7246 (mmt) REVERT: A 120 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: D 210 ASN cc_start: 0.8614 (t0) cc_final: 0.8292 (t0) REVERT: G 338 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7509 (ttt-90) REVERT: H 49 GLU cc_start: 0.8355 (tp30) cc_final: 0.8013 (tp30) REVERT: H 96 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7284 (mt-10) outliers start: 21 outliers final: 13 residues processed: 184 average time/residue: 0.7353 time to fit residues: 146.5138 Evaluate side-chains 179 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 320 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 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 H residue 96 GLU 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: 0.0870 chunk 41 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3342 r_free = 0.3342 target = 0.104939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083474 restraints weight = 46622.134| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.39 r_work: 0.2864 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 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 = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14766 Z= 0.161 Angle : 0.584 13.507 20001 Z= 0.305 Chirality : 0.044 0.171 2082 Planarity : 0.004 0.047 2634 Dihedral : 4.760 45.609 1992 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 1.38 % Allowed : 21.67 % 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: 0.75 (0.20), residues: 1773 helix: 1.19 (0.23), residues: 555 sheet: 0.44 (0.29), residues: 306 loop : 0.21 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 146 TYR 0.011 0.001 TYR B 45 PHE 0.034 0.002 PHE B 277 TRP 0.028 0.002 TRP D 429 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (14754) covalent geometry : angle 0.57604 / 0.30 (19992) hydrogen bonds : bond 0.04384 / 2.88 ( 629) hydrogen bonds : angle 4.57217 / 3.17 ( 1944) metal coordination : bond 0.01370 / 0.87 ( 12) metal coordination : angle 4.69009 / 2.53 ( 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 186 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.607 Fit side-chains REVERT: B 180 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8260 (ttp) REVERT: B 338 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7887 (ttt-90) REVERT: B 437 MET cc_start: 0.7553 (mmt) cc_final: 0.7261 (mmt) REVERT: A 120 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: G 338 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7520 (ttt-90) REVERT: H 49 GLU cc_start: 0.8363 (tp30) cc_final: 0.8015 (tp30) REVERT: H 96 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7249 (mt-10) outliers start: 21 outliers final: 13 residues processed: 175 average time/residue: 0.7688 time to fit residues: 145.4939 Evaluate side-chains 183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 320 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 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 H residue 96 GLU 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: 0.8980 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3396 r_free = 0.3396 target = 0.108319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086584 restraints weight = 55694.415| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.69 r_work: 0.2914 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14766 Z= 0.100 Angle : 0.538 12.847 20001 Z= 0.277 Chirality : 0.042 0.149 2082 Planarity : 0.004 0.043 2634 Dihedral : 4.519 45.366 1992 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 0.99 % Allowed : 22.07 % 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: 0.93 (0.20), residues: 1773 helix: 1.37 (0.23), residues: 555 sheet: 0.38 (0.28), residues: 309 loop : 0.37 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 146 TYR 0.013 0.001 TYR G 426 PHE 0.032 0.001 PHE B 277 TRP 0.030 0.001 TRP D 429 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (14754) covalent geometry : angle 0.52908 / 0.28 (19992) hydrogen bonds : bond 0.03397 / 2.24 ( 629) hydrogen bonds : angle 4.21275 / 2.92 ( 1944) metal coordination : bond 0.00467 / 0.29 ( 12) metal coordination : angle 4.65661 / 2.53 ( 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: 15 poor density : 182 time to evaluate : 0.581 Fit side-chains REVERT: B 338 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7841 (ttt-90) REVERT: B 437 MET cc_start: 0.7640 (mmt) cc_final: 0.7290 (mmt) REVERT: A 120 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: D 210 ASN cc_start: 0.8463 (t0) cc_final: 0.8106 (t0) REVERT: D 426 TYR cc_start: 0.8234 (m-80) cc_final: 0.7867 (m-80) REVERT: G 338 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7481 (ttt-90) REVERT: H 49 GLU cc_start: 0.8357 (tp30) cc_final: 0.8021 (tp30) outliers start: 15 outliers final: 6 residues processed: 188 average time/residue: 0.7583 time to fit residues: 154.3782 Evaluate side-chains 181 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 320 THR 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 H residue 116 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3351 r_free = 0.3351 target = 0.105478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083399 restraints weight = 58826.633| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.75 r_work: 0.2857 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14766 Z= 0.154 Angle : 0.584 12.841 20001 Z= 0.303 Chirality : 0.044 0.183 2082 Planarity : 0.004 0.045 2634 Dihedral : 4.665 44.358 1992 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 0.79 % Allowed : 22.53 % Favored : 76.68 % 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: 0.85 (0.20), residues: 1773 helix: 1.25 (0.23), residues: 555 sheet: 0.34 (0.27), residues: 336 loop : 0.36 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 146 TYR 0.011 0.001 TYR B 45 PHE 0.032 0.002 PHE B 277 TRP 0.030 0.002 TRP D 429 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (14754) covalent geometry : angle 0.57599 / 0.30 (19992) hydrogen bonds : bond 0.04258 / 2.80 ( 629) hydrogen bonds : angle 4.49464 / 3.12 ( 1944) metal coordination : bond 0.01206 / 0.78 ( 12) metal coordination : angle 4.67654 / 2.52 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5042.96 seconds wall clock time: 86 minutes 51.54 seconds (5211.54 seconds total)