Starting phenix.real_space_refine on Thu Jun 12 18:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2t_34443/06_2025/8h2t_34443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2t_34443/06_2025/8h2t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h2t_34443/06_2025/8h2t_34443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2t_34443/06_2025/8h2t_34443.map" model { file = "/net/cci-nas-00/data/ceres_data/8h2t_34443/06_2025/8h2t_34443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2t_34443/06_2025/8h2t_34443.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.90, per 1000 atoms: 0.97 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: 3.69 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 501 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 87 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 109 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 106 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 85 " pdb=" FES D 501 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 87 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 106 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 85 " pdb=" FES G 501 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 87 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 109 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 85 " Number of angles added : 9 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 37.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 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: 4.95 Time building geometry restraints manager: 4.22 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 437 or resid 501 throug \ h 503)) selection = (chain 'D' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) selection = (chain 'G' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 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: 0.730 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.330 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14766 Z= 0.145 Angle : 0.597 12.109 20001 Z= 0.320 Chirality : 0.043 0.151 2082 Planarity : 0.005 0.043 2634 Dihedral : 16.316 84.781 5412 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 21.54 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 PHE 0.039 0.001 PHE B 277 TYR 0.013 0.001 TYR G 426 ARG 0.004 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.12186 ( 629) hydrogen bonds : angle 6.17027 ( 1944) metal coordination : bond 0.00705 ( 12) metal coordination : angle 4.78625 ( 9) covalent geometry : bond 0.00318 (14754) covalent geometry : angle 0.58831 (19992) *********************** 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 : 1.665 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: 1.5138 time to fit residues: 308.6708 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 : 1.725 ------------------------------------------------------------------------------- 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 146 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082199 restraints weight = 49249.932| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.46 r_work: 0.2845 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14766 Z= 0.177 Angle : 0.581 8.818 20001 Z= 0.307 Chirality : 0.044 0.158 2082 Planarity : 0.005 0.047 2634 Dihedral : 6.091 58.500 2028 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 2.37 % Allowed : 19.96 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1773 helix: 0.96 (0.23), residues: 552 sheet: 0.29 (0.28), residues: 336 loop : 0.07 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 429 HIS 0.005 0.001 HIS G 311 PHE 0.032 0.002 PHE B 277 TYR 0.014 0.001 TYR D 426 ARG 0.004 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 629) hydrogen bonds : angle 4.88870 ( 1944) metal coordination : bond 0.01574 ( 12) metal coordination : angle 4.72677 ( 9) covalent geometry : bond 0.00415 (14754) covalent geometry : angle 0.57220 (19992) *********************** 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 209 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: B 437 MET cc_start: 0.7725 (mmt) cc_final: 0.7500 (mmt) REVERT: D 209 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: G 19 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7475 (ptt-90) REVERT: G 338 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7559 (ttt-90) REVERT: H 49 GLU cc_start: 0.8197 (tp30) cc_final: 0.7989 (tp30) outliers start: 36 outliers final: 6 residues processed: 196 average time/residue: 1.5945 time to fit residues: 336.9594 Evaluate side-chains 172 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 122 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.079839 restraints weight = 59297.249| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.75 r_work: 0.2795 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14766 Z= 0.279 Angle : 0.654 11.100 20001 Z= 0.346 Chirality : 0.048 0.179 2082 Planarity : 0.005 0.048 2634 Dihedral : 5.507 57.674 1996 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 2.17 % Allowed : 20.29 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1773 helix: 0.79 (0.23), residues: 552 sheet: 0.42 (0.29), residues: 306 loop : -0.11 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 429 HIS 0.007 0.001 HIS G 311 PHE 0.032 0.002 PHE B 277 TYR 0.016 0.002 TYR D 426 ARG 0.005 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.05758 ( 629) hydrogen bonds : angle 5.12693 ( 1944) metal coordination : bond 0.02745 ( 12) metal coordination : angle 4.66180 ( 9) covalent geometry : bond 0.00668 (14754) covalent geometry : angle 0.64641 (19992) *********************** 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 195 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: B 180 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8329 (ttp) REVERT: B 338 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7915 (ttt-90) REVERT: B 437 MET cc_start: 0.7571 (mmt) cc_final: 0.7310 (mmt) REVERT: A 120 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: D 52 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (pp) REVERT: D 437 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6777 (mmm) REVERT: G 19 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7424 (ptt-90) REVERT: G 338 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7570 (ttt-90) REVERT: H 49 GLU cc_start: 0.8333 (tp30) cc_final: 0.8096 (tp30) outliers start: 33 outliers final: 11 residues processed: 180 average time/residue: 1.6651 time to fit residues: 323.0940 Evaluate side-chains 178 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082275 restraints weight = 50010.807| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.51 r_work: 0.2843 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 0.039 14766 Z= 0.164 Angle : 0.572 10.275 20001 Z= 0.303 Chirality : 0.044 0.158 2082 Planarity : 0.005 0.046 2634 Dihedral : 5.252 51.994 1995 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 20.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1773 helix: 1.00 (0.23), residues: 552 sheet: 0.22 (0.28), residues: 336 loop : -0.05 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 429 HIS 0.004 0.001 HIS G 311 PHE 0.033 0.002 PHE B 277 TYR 0.012 0.001 TYR D 426 ARG 0.004 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 629) hydrogen bonds : angle 4.75188 ( 1944) metal coordination : bond 0.01500 ( 12) metal coordination : angle 4.46176 ( 9) covalent geometry : bond 0.00384 (14754) covalent geometry : angle 0.56396 (19992) *********************** 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 200 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.738 Fit side-chains REVERT: B 180 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8224 (ttp) REVERT: B 338 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7909 (ttt-90) REVERT: B 437 MET cc_start: 0.7633 (mmt) cc_final: 0.7411 (mmt) REVERT: A 120 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: D 209 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: D 437 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6773 (mmm) REVERT: G 19 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7468 (ptt-90) REVERT: G 34 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7038 (pt0) REVERT: G 338 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7507 (ttt-90) REVERT: H 49 GLU cc_start: 0.8307 (tp30) cc_final: 0.8030 (tp30) outliers start: 32 outliers final: 8 residues processed: 188 average time/residue: 1.8973 time to fit residues: 383.7464 Evaluate side-chains 178 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain 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 209 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081886 restraints weight = 57493.953| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.65 r_work: 0.2847 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14766 Z= 0.148 Angle : 0.563 10.697 20001 Z= 0.296 Chirality : 0.044 0.170 2082 Planarity : 0.004 0.045 2634 Dihedral : 5.126 49.578 1995 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 1.91 % Allowed : 20.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1773 helix: 1.07 (0.23), residues: 555 sheet: 0.24 (0.28), residues: 336 loop : 0.04 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 PHE 0.035 0.001 PHE B 277 TYR 0.011 0.001 TYR B 45 ARG 0.004 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 629) hydrogen bonds : angle 4.62140 ( 1944) metal coordination : bond 0.01271 ( 12) metal coordination : angle 4.49653 ( 9) covalent geometry : bond 0.00345 (14754) covalent geometry : angle 0.55544 (19992) *********************** 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 201 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.739 Fit side-chains REVERT: B 180 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8234 (ttp) REVERT: B 255 TYR cc_start: 0.8240 (m-80) cc_final: 0.7421 (m-80) REVERT: B 308 MET cc_start: 0.6770 (mtp) cc_final: 0.6457 (ttt) REVERT: B 338 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7873 (ttt-90) REVERT: B 437 MET cc_start: 0.7631 (mmt) cc_final: 0.7355 (mmt) REVERT: A 96 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7990 (mt-10) REVERT: A 120 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: D 437 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6560 (mmm) REVERT: G 19 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7465 (ptt-90) REVERT: G 34 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7020 (pt0) REVERT: G 338 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7542 (ttt-90) REVERT: H 49 GLU cc_start: 0.8330 (tp30) cc_final: 0.8035 (tp30) outliers start: 29 outliers final: 12 residues processed: 187 average time/residue: 1.6962 time to fit residues: 341.6963 Evaluate side-chains 181 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083130 restraints weight = 37732.153| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.08 r_work: 0.2866 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14766 Z= 0.174 Angle : 0.587 11.552 20001 Z= 0.307 Chirality : 0.045 0.159 2082 Planarity : 0.005 0.044 2634 Dihedral : 4.897 46.335 1992 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 20.69 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1773 helix: 1.04 (0.23), residues: 555 sheet: 0.44 (0.29), residues: 306 loop : 0.05 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 429 HIS 0.004 0.001 HIS G 311 PHE 0.032 0.002 PHE B 277 TYR 0.012 0.001 TYR B 45 ARG 0.006 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 629) hydrogen bonds : angle 4.69780 ( 1944) metal coordination : bond 0.01573 ( 12) metal coordination : angle 4.58657 ( 9) covalent geometry : bond 0.00413 (14754) covalent geometry : angle 0.57857 (19992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 2.076 Fit side-chains revert: symmetry clash REVERT: B 180 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: B 308 MET cc_start: 0.6978 (mtp) cc_final: 0.6699 (ttt) REVERT: B 338 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7884 (ttt-90) REVERT: B 437 MET cc_start: 0.7636 (mmt) cc_final: 0.7413 (mmt) REVERT: A 104 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7168 (mtm110) REVERT: A 120 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8260 (mm-30) REVERT: D 437 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6530 (mmm) REVERT: G 19 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7457 (ptt-90) REVERT: G 34 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7030 (pt0) REVERT: G 338 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7537 (ttt-90) REVERT: H 49 GLU cc_start: 0.8343 (tp30) cc_final: 0.8053 (tp30) outliers start: 32 outliers final: 16 residues processed: 184 average time/residue: 1.6718 time to fit residues: 332.1486 Evaluate side-chains 187 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 81 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 15 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.084321 restraints weight = 44353.823| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.34 r_work: 0.2885 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0954 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= 0.125 Angle : 0.552 11.688 20001 Z= 0.287 Chirality : 0.043 0.145 2082 Planarity : 0.004 0.043 2634 Dihedral : 4.711 46.074 1992 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 1.71 % Allowed : 20.95 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1773 helix: 1.18 (0.23), residues: 555 sheet: 0.29 (0.28), residues: 336 loop : 0.16 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 PHE 0.031 0.001 PHE B 277 TYR 0.009 0.001 TYR B 45 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 629) hydrogen bonds : angle 4.44845 ( 1944) metal coordination : bond 0.00952 ( 12) metal coordination : angle 4.53152 ( 9) covalent geometry : bond 0.00286 (14754) covalent geometry : angle 0.54348 (19992) *********************** 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 200 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.503 Fit side-chains REVERT: B 338 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7868 (ttt-90) REVERT: B 437 MET cc_start: 0.7679 (mmt) cc_final: 0.7437 (mmt) REVERT: A 96 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 120 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: D 210 ASN cc_start: 0.8628 (t0) cc_final: 0.8324 (t0) REVERT: G 19 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7467 (ptt-90) REVERT: G 338 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7523 (ttt-90) REVERT: H 49 GLU cc_start: 0.8311 (tp30) cc_final: 0.8010 (tp30) outliers start: 26 outliers final: 9 residues processed: 186 average time/residue: 1.4806 time to fit residues: 298.4318 Evaluate side-chains 176 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 145 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.084541 restraints weight = 52748.986| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.60 r_work: 0.2884 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14766 Z= 0.117 Angle : 0.549 11.993 20001 Z= 0.284 Chirality : 0.043 0.147 2082 Planarity : 0.004 0.043 2634 Dihedral : 4.612 44.964 1992 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 1.25 % Allowed : 21.87 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1773 helix: 1.27 (0.23), residues: 555 sheet: 0.44 (0.29), residues: 306 loop : 0.25 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.030 0.001 PHE B 277 TYR 0.009 0.001 TYR B 45 ARG 0.004 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 629) hydrogen bonds : angle 4.35399 ( 1944) metal coordination : bond 0.00834 ( 12) metal coordination : angle 4.66431 ( 9) covalent geometry : bond 0.00267 (14754) covalent geometry : angle 0.53998 (19992) *********************** 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 189 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.513 Fit side-chains REVERT: B 338 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7863 (ttt-90) REVERT: B 437 MET cc_start: 0.7687 (mmt) cc_final: 0.7444 (mmt) REVERT: A 104 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7165 (mtm110) REVERT: A 120 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: D 210 ASN cc_start: 0.8565 (t0) cc_final: 0.8253 (t0) REVERT: G 338 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7498 (ttt-90) REVERT: G 422 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7185 (mpt) REVERT: H 49 GLU cc_start: 0.8356 (tp30) cc_final: 0.8048 (tp30) outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 1.5344 time to fit residues: 297.0022 Evaluate side-chains 173 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 A residue 104 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 105 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.084100 restraints weight = 56158.290| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.68 r_work: 0.2874 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14766 Z= 0.125 Angle : 0.557 12.358 20001 Z= 0.289 Chirality : 0.043 0.151 2082 Planarity : 0.004 0.043 2634 Dihedral : 4.617 44.605 1992 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 0.99 % Allowed : 22.27 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1773 helix: 1.29 (0.23), residues: 555 sheet: 0.40 (0.29), residues: 309 loop : 0.24 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.029 0.001 PHE B 277 TYR 0.011 0.001 TYR B 426 ARG 0.004 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 629) hydrogen bonds : angle 4.38346 ( 1944) metal coordination : bond 0.00908 ( 12) metal coordination : angle 4.66669 ( 9) covalent geometry : bond 0.00289 (14754) covalent geometry : angle 0.54790 (19992) *********************** 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 183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.764 Fit side-chains REVERT: B 338 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7856 (ttt-90) REVERT: B 437 MET cc_start: 0.7692 (mmt) cc_final: 0.7405 (mmt) REVERT: A 104 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7165 (mtm110) REVERT: A 120 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8279 (mm-30) REVERT: D 210 ASN cc_start: 0.8595 (t0) cc_final: 0.8259 (t0) REVERT: D 437 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6873 (mmp) REVERT: G 19 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7536 (ptt-90) REVERT: G 338 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7497 (ttt-90) REVERT: H 49 GLU cc_start: 0.8367 (tp30) cc_final: 0.8058 (tp30) outliers start: 15 outliers final: 7 residues processed: 176 average time/residue: 1.5986 time to fit residues: 303.9642 Evaluate side-chains 176 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 A residue 104 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 437 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 11 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087270 restraints weight = 55422.732| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.64 r_work: 0.2926 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14766 Z= 0.097 Angle : 0.527 12.246 20001 Z= 0.272 Chirality : 0.042 0.160 2082 Planarity : 0.004 0.040 2634 Dihedral : 4.425 43.769 1992 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 0.66 % Allowed : 22.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1773 helix: 1.42 (0.23), residues: 555 sheet: 0.33 (0.27), residues: 339 loop : 0.36 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 429 HIS 0.003 0.001 HIS G 216 PHE 0.039 0.001 PHE B 277 TYR 0.011 0.001 TYR G 426 ARG 0.003 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 629) hydrogen bonds : angle 4.12702 ( 1944) metal coordination : bond 0.00434 ( 12) metal coordination : angle 4.62385 ( 9) covalent geometry : bond 0.00212 (14754) covalent geometry : angle 0.51767 (19992) ********************** 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 191 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 1.639 Fit side-chains REVERT: B 437 MET cc_start: 0.7769 (mmt) cc_final: 0.7438 (mmt) REVERT: A 120 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: D 210 ASN cc_start: 0.8535 (t0) cc_final: 0.8252 (t0) REVERT: D 426 TYR cc_start: 0.8379 (m-80) cc_final: 0.8148 (m-80) REVERT: G 338 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7423 (ttt-90) REVERT: H 49 GLU cc_start: 0.8335 (tp30) cc_final: 0.8022 (tp30) outliers start: 10 outliers final: 6 residues processed: 186 average time/residue: 1.5388 time to fit residues: 309.9565 Evaluate side-chains 180 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 126 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.082233 restraints weight = 67263.861| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.95 r_work: 0.2836 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14766 Z= 0.178 Angle : 0.607 13.645 20001 Z= 0.314 Chirality : 0.045 0.177 2082 Planarity : 0.004 0.046 2634 Dihedral : 4.733 44.154 1992 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 0.86 % Allowed : 22.79 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1773 helix: 1.20 (0.23), residues: 555 sheet: 0.38 (0.27), residues: 336 loop : 0.29 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 429 HIS 0.005 0.001 HIS G 311 PHE 0.037 0.002 PHE B 277 TYR 0.011 0.002 TYR B 45 ARG 0.005 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 629) hydrogen bonds : angle 4.56635 ( 1944) metal coordination : bond 0.01538 ( 12) metal coordination : angle 4.63427 ( 9) covalent geometry : bond 0.00422 (14754) covalent geometry : angle 0.59865 (19992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11106.49 seconds wall clock time: 194 minutes 48.12 seconds (11688.12 seconds total)