Starting phenix.real_space_refine on Sat Aug 8 13:11:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2026/8bd5_15975.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 346 5.49 5 Mg 7 5.21 5 S 85 5.16 5 C 16621 2.51 5 N 5150 2.21 5 O 6187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28398 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4899 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Chain: "B" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 5235 Classifications: {'RNAv2': 246} Modifications used: {'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 106, 'rna3p_pyr': 102} Link IDs: {'rna2p': 38, 'rna3p': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 827 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "D" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 840 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2046 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1284 Classifications: {'peptide': 161} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 148} Chain: "X" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 685 Classifications: {'peptide': 85} Link IDs: {'TRANS': 84} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27217 SG CYS Q 133 72.612 119.769 107.506 1.00 71.20 S ATOM 27238 SG CYS Q 136 75.671 117.734 106.864 1.00 77.14 S ATOM 27354 SG CYS Q 151 72.278 116.157 107.379 1.00 78.37 S ATOM 27381 SG CYS Q 154 73.864 117.713 110.203 1.00 81.82 S ATOM 26942 SG CYS Q 100 60.616 127.373 106.385 1.00 74.10 S ATOM 26957 SG CYS Q 103 56.645 126.988 106.822 1.00 77.88 S ATOM 27126 SG CYS Q 122 57.843 129.425 104.971 1.00 82.85 S Time building chain proxies: 6.28, per 1000 atoms: 0.22 Number of scatterers: 28398 At special positions: 0 Unit cell: (136.5, 150.15, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 85 16.00 P 346 15.00 Mg 7 11.99 O 6187 8.00 N 5150 7.00 C 16621 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: 2.80 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 154 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 136 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 151 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 133 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 125 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 103 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 100 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 122 " Number of angles added : 9 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5028 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 13 sheets defined 63.4% alpha, 5.7% beta 118 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.791A pdb=" N LEU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.416A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.704A pdb=" N SER A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.547A pdb=" N ASN A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 233 removed outlier: 3.702A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.691A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 318 through 338 removed outlier: 4.468A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 408 removed outlier: 3.583A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 removed outlier: 4.201A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.729A pdb=" N LEU A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 507 removed outlier: 4.150A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 538 Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.555A pdb=" N VAL A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'A' and resid 618 through 635 Processing helix chain 'E' and resid 18 through 30 Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.698A pdb=" N LYS E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.730A pdb=" N ALA E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.617A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 137 Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 150 through 165 removed outlier: 3.568A pdb=" N PHE E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.635A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.863A pdb=" N LEU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 215 removed outlier: 3.645A pdb=" N ASN E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 215 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 240 through 259 Processing helix chain 'E' and resid 264 through 276 removed outlier: 3.686A pdb=" N LEU E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 30 removed outlier: 3.998A pdb=" N GLY F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 67 through 77 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'F' and resid 173 through 181 removed outlier: 3.791A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 202 through 214 removed outlier: 4.116A pdb=" N ASN F 206 " --> pdb=" O GLU F 202 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 3.815A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 264 through 276 Processing helix chain 'G' and resid 18 through 30 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 removed outlier: 3.578A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG G 74 " --> pdb=" O CYS G 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS G 77 " --> pdb=" O TYR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.737A pdb=" N LEU G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 137 Processing helix chain 'G' and resid 146 through 149 removed outlier: 3.582A pdb=" N LEU G 149 " --> pdb=" O ALA G 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 146 through 149' Processing helix chain 'G' and resid 150 through 165 removed outlier: 3.631A pdb=" N PHE G 154 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 183 removed outlier: 4.203A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 226 through 237 removed outlier: 4.110A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 233 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA G 236 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 276 removed outlier: 3.656A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 30 Processing helix chain 'H' and resid 36 through 52 removed outlier: 3.738A pdb=" N ALA H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.900A pdb=" N HIS H 77 " --> pdb=" O TYR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.528A pdb=" N LEU H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 136 Processing helix chain 'H' and resid 152 through 165 removed outlier: 4.190A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 182 removed outlier: 3.630A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'H' and resid 201 through 215 removed outlier: 3.639A pdb=" N LYS H 205 " --> pdb=" O GLY H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 238 Processing helix chain 'H' and resid 240 through 258 Processing helix chain 'H' and resid 264 through 274 Processing helix chain 'I' and resid 18 through 30 removed outlier: 3.660A pdb=" N GLY I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 52 removed outlier: 3.540A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 150 through 165 removed outlier: 3.776A pdb=" N PHE I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA I 155 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP I 156 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 183 removed outlier: 4.061A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.510A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.588A pdb=" N GLU I 238 " --> pdb=" O THR I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 259 Processing helix chain 'I' and resid 264 through 274 Processing helix chain 'J' and resid 18 through 30 Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 removed outlier: 4.044A pdb=" N HIS J 77 " --> pdb=" O TYR J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.806A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 Processing helix chain 'J' and resid 150 through 165 removed outlier: 3.831A pdb=" N PHE J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 183 removed outlier: 3.654A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP J 183 " --> pdb=" O VAL J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 201 through 215 Processing helix chain 'J' and resid 226 through 237 Processing helix chain 'J' and resid 240 through 258 Processing helix chain 'J' and resid 264 through 274 Processing helix chain 'K' and resid 18 through 30 Processing helix chain 'K' and resid 36 through 51 Processing helix chain 'K' and resid 65 through 77 removed outlier: 3.512A pdb=" N ALA K 69 " --> pdb=" O GLY K 65 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS K 77 " --> pdb=" O TYR K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.530A pdb=" N LEU K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 137 Processing helix chain 'K' and resid 150 through 152 No H-bonds generated for 'chain 'K' and resid 150 through 152' Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 173 through 182 removed outlier: 4.040A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 190 removed outlier: 3.701A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 214 Processing helix chain 'K' and resid 226 through 238 Processing helix chain 'K' and resid 240 through 258 Processing helix chain 'K' and resid 264 through 276 removed outlier: 3.759A pdb=" N LEU K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 34 Processing helix chain 'Q' and resid 36 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 63 through 75 removed outlier: 3.827A pdb=" N ILE Q 70 " --> pdb=" O GLU Q 66 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 83 Processing helix chain 'Q' and resid 100 through 107 Processing helix chain 'Q' and resid 111 through 116 Processing helix chain 'Q' and resid 142 through 146 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 3.539A pdb=" N ALA Q 162 " --> pdb=" O ALA Q 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 15 Processing helix chain 'X' and resid 24 through 46 removed outlier: 4.275A pdb=" N GLY X 41 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS X 42 " --> pdb=" O HIS X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 74 removed outlier: 4.112A pdb=" N GLY X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 291 through 295 removed outlier: 5.030A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 305 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 311 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 452 removed outlier: 6.042A pdb=" N ASP A 465 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 471 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 542 through 546 removed outlier: 6.220A pdb=" N ILE A 543 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY A 611 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 545 " --> pdb=" O GLY A 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 58 through 59 Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.152A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP E 144 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 94 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU E 141 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL E 171 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 143 " --> pdb=" O VAL E 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 59 removed outlier: 7.168A pdb=" N CYS F 56 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 59 through 60 removed outlier: 7.887A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.475A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP G 144 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE G 94 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL G 171 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE G 143 " --> pdb=" O VAL G 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.303A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU H 170 " --> pdb=" O CYS H 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.399A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY I 172 " --> pdb=" O VAL I 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 56 through 59 removed outlier: 3.864A pdb=" N LEU J 194 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 91 through 94 removed outlier: 5.749A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU J 141 " --> pdb=" O VAL J 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.349A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5624 1.33 - 1.45: 8100 1.45 - 1.57: 15030 1.57 - 1.69: 684 1.69 - 1.81: 126 Bond restraints: 29564 Sorted by residual: bond pdb=" N PRO I 79 " pdb=" CD PRO I 79 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C3' DA D 14 " pdb=" C2' DA D 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 bond pdb=" C3' DT D 12 " pdb=" C2' DT D 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.69e+00 bond pdb=" N ASN Q 59 " pdb=" CA ASN Q 59 " ideal model delta sigma weight residual 1.462 1.489 -0.028 9.50e-03 1.11e+04 8.58e+00 bond pdb=" N LYS F 66 " pdb=" CA LYS F 66 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.47e+00 ... (remaining 29559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 39668 1.81 - 3.62: 1568 3.62 - 5.44: 197 5.44 - 7.25: 23 7.25 - 9.06: 5 Bond angle restraints: 41461 Sorted by residual: angle pdb=" O4' DT C -14 " pdb=" C4' DT C -14 " pdb=" C3' DT C -14 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" O4' DC C -32 " pdb=" C4' DC C -32 " pdb=" C3' DC C -32 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.56e+01 angle pdb=" O4' DA C -15 " pdb=" C4' DA C -15 " pdb=" C3' DA C -15 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" C3' A B 130 " pdb=" O3' A B 130 " pdb=" P G B 131 " ideal model delta sigma weight residual 119.70 125.41 -5.71 1.20e+00 6.94e-01 2.26e+01 angle pdb=" N3 DT C -28 " pdb=" C4 DT C -28 " pdb=" O4 DT C -28 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 ... (remaining 41456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 15771 35.96 - 71.93: 1389 71.93 - 107.89: 64 107.89 - 143.86: 4 143.86 - 179.82: 7 Dihedral angle restraints: 17235 sinusoidal: 9476 harmonic: 7759 Sorted by residual: dihedral pdb=" C4' A B 50 " pdb=" C3' A B 50 " pdb=" C2' A B 50 " pdb=" C1' A B 50 " ideal model delta sinusoidal sigma weight residual 36.34 -41.01 77.35 1 3.10e+00 1.04e-01 7.80e+02 dihedral pdb=" C4' U B 44 " pdb=" C3' U B 44 " pdb=" C2' U B 44 " pdb=" C1' U B 44 " ideal model delta sinusoidal sigma weight residual 36.34 -39.34 75.68 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' A B 22 " pdb=" C3' A B 22 " pdb=" C2' A B 22 " pdb=" C1' A B 22 " ideal model delta sinusoidal sigma weight residual 36.34 -39.01 75.36 1 3.10e+00 1.04e-01 7.46e+02 ... (remaining 17232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4230 0.087 - 0.173: 287 0.173 - 0.260: 266 0.260 - 0.346: 55 0.346 - 0.433: 2 Chirality restraints: 4840 Sorted by residual: chirality pdb=" P G B 15 " pdb=" OP1 G B 15 " pdb=" OP2 G B 15 " pdb=" O5' G B 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.61 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" P A B 51 " pdb=" OP1 A B 51 " pdb=" OP2 A B 51 " pdb=" O5' A B 51 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" P G B 131 " pdb=" OP1 G B 131 " pdb=" OP2 G B 131 " pdb=" O5' G B 131 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 4837 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 89 " -0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO H 90 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO H 90 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 90 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 59 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C ASN Q 59 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN Q 59 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO Q 60 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 213 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" CD GLN F 213 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN F 213 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN F 213 " 0.014 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 293 2.57 - 3.15: 22967 3.15 - 3.73: 52082 3.73 - 4.32: 67641 4.32 - 4.90: 102688 Nonbonded interactions: 245671 Sorted by model distance: nonbonded pdb=" O1B ATP J 301 " pdb="MG MG J 302 " model vdw 1.983 2.170 nonbonded pdb=" O1B ATP K 301 " pdb="MG MG K 302 " model vdw 1.986 2.170 nonbonded pdb=" OG1 THR J 67 " pdb="MG MG J 302 " model vdw 2.040 2.170 nonbonded pdb=" O1G ATP K 301 " pdb="MG MG K 302 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP G 301 " pdb="MG MG G 302 " model vdw 2.082 2.170 ... (remaining 245666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 302 \ )) selection = (chain 'F' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'G' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 302 \ )) selection = (chain 'H' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 302 \ )) selection = (chain 'I' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 302 \ )) selection = (chain 'J' and (resid 17 through 260 or (resid 261 through 264 and (name N or na \ me CA or name C or name O or name CB )) or resid 265 through 302)) selection = (chain 'K' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 260 or (resid 261 through 264 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 302 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.920 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.004 0.078 29572 Z= 0.274 Angle : 0.776 19.395 41470 Z= 0.444 Chirality : 0.074 0.433 4840 Planarity : 0.004 0.096 4076 Dihedral : 21.903 179.825 12207 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 0.76 % Allowed : 27.00 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2649 helix: 0.96 (0.13), residues: 1524 sheet: -1.61 (0.43), residues: 141 loop : -1.09 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 128 TYR 0.024 0.002 TYR H 73 PHE 0.013 0.001 PHE F 204 TRP 0.013 0.002 TRP J 45 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.27 (29564) covalent geometry : angle 0.76614 / 0.44 (41461) hydrogen bonds : bond 0.12553 / 8.20 ( 1455) hydrogen bonds : angle 5.61562 / 4.02 ( 3996) metal coordination : bond 0.05872 / 3.68 ( 8) metal coordination : angle 8.24840 / 5.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: F 145 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: H 45 TRP cc_start: 0.3490 (OUTLIER) cc_final: 0.3140 (t60) outliers start: 17 outliers final: 5 residues processed: 114 average time/residue: 0.2027 time to fit residues: 37.0367 Evaluate side-chains 107 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain H residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 80 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN Q 59 ASN Q 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.082021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057270 restraints weight = 135229.721| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.41 r_work: 0.3259 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29572 Z= 0.224 Angle : 1.085 20.505 41470 Z= 0.467 Chirality : 0.109 1.530 4840 Planarity : 0.005 0.074 4076 Dihedral : 19.965 179.107 6858 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 25.88 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2649 helix: 1.01 (0.13), residues: 1549 sheet: -1.64 (0.43), residues: 143 loop : -1.08 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 243 TYR 0.022 0.002 TYR H 73 PHE 0.017 0.002 PHE H 106 TRP 0.014 0.001 TRP A 21 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (29564) covalent geometry : angle 1.08438 / 0.47 (41461) hydrogen bonds : bond 0.04935 / 3.23 ( 1455) hydrogen bonds : angle 4.48936 / 3.21 ( 3996) metal coordination : bond 0.01065 / 0.61 ( 8) metal coordination : angle 2.73437 / 1.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 101 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8038 (t0) REVERT: A 322 LEU cc_start: 0.8745 (tp) cc_final: 0.8462 (mt) REVERT: F 147 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: G 98 GLN cc_start: 0.8290 (tp40) cc_final: 0.7927 (tp40) REVERT: G 149 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7309 (pp) REVERT: G 205 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6961 (pttt) REVERT: H 73 TYR cc_start: 0.6375 (t80) cc_final: 0.6087 (t80) REVERT: I 108 LYS cc_start: 0.7347 (mtpt) cc_final: 0.6978 (mtpp) outliers start: 57 outliers final: 25 residues processed: 150 average time/residue: 0.1850 time to fit residues: 45.4767 Evaluate side-chains 126 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 24 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 200 optimal weight: 50.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.082590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.056283 restraints weight = 135598.889| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.46 r_work: 0.3310 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29572 Z= 0.168 Angle : 0.880 16.960 41470 Z= 0.391 Chirality : 0.080 1.316 4840 Planarity : 0.004 0.061 4076 Dihedral : 20.021 177.574 6842 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.08 % Allowed : 25.17 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2649 helix: 1.17 (0.13), residues: 1549 sheet: -1.56 (0.42), residues: 142 loop : -1.01 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 243 TYR 0.022 0.002 TYR K 75 PHE 0.015 0.001 PHE J 204 TRP 0.014 0.001 TRP G 45 HIS 0.008 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (29564) covalent geometry : angle 0.87985 / 0.39 (41461) hydrogen bonds : bond 0.04172 / 2.74 ( 1455) hydrogen bonds : angle 4.16939 / 2.98 ( 3996) metal coordination : bond 0.00637 / 0.33 ( 8) metal coordination : angle 2.17648 / 1.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 111 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8109 (t0) REVERT: F 103 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8285 (tttp) REVERT: F 275 TYR cc_start: 0.7202 (t80) cc_final: 0.6882 (t80) REVERT: G 75 TYR cc_start: 0.9086 (m-80) cc_final: 0.8708 (m-80) REVERT: G 98 GLN cc_start: 0.8240 (tp40) cc_final: 0.7872 (tp40) REVERT: G 106 PHE cc_start: 0.8890 (m-80) cc_final: 0.8561 (m-80) REVERT: H 56 CYS cc_start: 0.6904 (p) cc_final: 0.6598 (p) REVERT: H 73 TYR cc_start: 0.6587 (t80) cc_final: 0.6330 (t80) REVERT: H 275 TYR cc_start: 0.1201 (m-80) cc_final: 0.0970 (m-80) REVERT: I 80 GLN cc_start: 0.3153 (OUTLIER) cc_final: 0.2909 (pm20) REVERT: I 116 ARG cc_start: 0.3527 (mpt180) cc_final: 0.2169 (tpp-160) REVERT: K 214 MET cc_start: 0.4073 (mpp) cc_final: 0.3209 (ptm) outliers start: 69 outliers final: 33 residues processed: 168 average time/residue: 0.1759 time to fit residues: 48.6899 Evaluate side-chains 136 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 156 MET Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 199 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 13 optimal weight: 30.0000 chunk 109 optimal weight: 40.0000 chunk 261 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 98 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.080613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.056585 restraints weight = 135121.030| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.26 r_work: 0.3217 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 29572 Z= 0.325 Angle : 0.982 22.350 41470 Z= 0.441 Chirality : 0.081 1.380 4840 Planarity : 0.005 0.063 4076 Dihedral : 19.939 179.636 6842 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.69 % Allowed : 24.45 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2649 helix: 0.79 (0.13), residues: 1553 sheet: -1.09 (0.33), residues: 244 loop : -1.24 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 243 TYR 0.040 0.002 TYR K 75 PHE 0.022 0.002 PHE A 567 TRP 0.016 0.002 TRP J 45 HIS 0.010 0.002 HIS Q 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.33 (29564) covalent geometry : angle 0.98126 / 0.44 (41461) hydrogen bonds : bond 0.05164 / 3.42 ( 1455) hydrogen bonds : angle 4.29899 / 3.07 ( 3996) metal coordination : bond 0.01097 / 0.62 ( 8) metal coordination : angle 2.88319 / 1.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 106 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8450 (t70) REVERT: A 513 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: E 196 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7624 (t80) REVERT: F 131 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: F 147 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: G 75 TYR cc_start: 0.9093 (m-80) cc_final: 0.8810 (m-80) REVERT: G 106 PHE cc_start: 0.8951 (m-80) cc_final: 0.8500 (m-80) REVERT: G 205 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6999 (pttt) REVERT: H 56 CYS cc_start: 0.7058 (p) cc_final: 0.6543 (p) REVERT: H 190 PHE cc_start: 0.5705 (m-10) cc_final: 0.5485 (m-10) REVERT: H 275 TYR cc_start: 0.1142 (m-80) cc_final: 0.0927 (m-80) REVERT: I 116 ARG cc_start: 0.3453 (mpt180) cc_final: 0.1988 (tpp-160) REVERT: J 34 VAL cc_start: 0.3567 (OUTLIER) cc_final: 0.3316 (t) REVERT: Q 163 LYS cc_start: 0.8873 (ptpp) cc_final: 0.8533 (ptpp) outliers start: 105 outliers final: 63 residues processed: 198 average time/residue: 0.1660 time to fit residues: 53.1421 Evaluate side-chains 171 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 101 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 223 optimal weight: 40.0000 chunk 202 optimal weight: 30.0000 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.082196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.056139 restraints weight = 134707.544| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.72 r_work: 0.3290 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29572 Z= 0.161 Angle : 0.828 17.004 41470 Z= 0.374 Chirality : 0.073 1.398 4840 Planarity : 0.004 0.055 4076 Dihedral : 19.839 176.987 6842 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.88 % Allowed : 25.66 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2649 helix: 1.09 (0.13), residues: 1554 sheet: -1.12 (0.34), residues: 229 loop : -1.07 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 128 TYR 0.022 0.002 TYR H 73 PHE 0.021 0.001 PHE H 106 TRP 0.014 0.001 TRP J 45 HIS 0.009 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (29564) covalent geometry : angle 0.82714 / 0.37 (41461) hydrogen bonds : bond 0.03867 / 2.56 ( 1455) hydrogen bonds : angle 4.07367 / 2.91 ( 3996) metal coordination : bond 0.00686 / 0.36 ( 8) metal coordination : angle 2.00331 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 110 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8140 (t0) REVERT: A 513 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: E 196 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7222 (t80) REVERT: F 131 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: F 147 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: F 275 TYR cc_start: 0.7263 (t80) cc_final: 0.6932 (t80) REVERT: G 75 TYR cc_start: 0.9095 (m-80) cc_final: 0.8858 (m-80) REVERT: G 106 PHE cc_start: 0.8878 (m-80) cc_final: 0.8522 (m-80) REVERT: H 56 CYS cc_start: 0.7175 (p) cc_final: 0.6794 (p) REVERT: I 80 GLN cc_start: 0.3098 (OUTLIER) cc_final: 0.2885 (pm20) REVERT: I 116 ARG cc_start: 0.3496 (mpt180) cc_final: 0.2175 (tpp-160) REVERT: J 34 VAL cc_start: 0.3502 (OUTLIER) cc_final: 0.3171 (t) REVERT: Q 163 LYS cc_start: 0.8904 (ptpp) cc_final: 0.8541 (ptpp) outliers start: 87 outliers final: 45 residues processed: 186 average time/residue: 0.1714 time to fit residues: 51.5193 Evaluate side-chains 158 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 PHE Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 272 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 164 optimal weight: 30.0000 chunk 265 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 268 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.080878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.058830 restraints weight = 135009.848| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.98 r_work: 0.3197 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29572 Z= 0.281 Angle : 0.900 17.633 41470 Z= 0.406 Chirality : 0.076 1.393 4840 Planarity : 0.005 0.068 4076 Dihedral : 19.786 179.200 6842 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.51 % Allowed : 25.35 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2649 helix: 0.91 (0.13), residues: 1552 sheet: -1.19 (0.34), residues: 229 loop : -1.15 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 116 TYR 0.026 0.002 TYR H 73 PHE 0.018 0.002 PHE A 567 TRP 0.016 0.002 TRP J 45 HIS 0.011 0.002 HIS K 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.28 (29564) covalent geometry : angle 0.89919 / 0.41 (41461) hydrogen bonds : bond 0.04606 / 3.06 ( 1455) hydrogen bonds : angle 4.14916 / 2.96 ( 3996) metal coordination : bond 0.00939 / 0.52 ( 8) metal coordination : angle 2.47142 / 1.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 107 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8165 (t0) REVERT: A 513 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: E 196 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7351 (t80) REVERT: F 131 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: F 147 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: F 276 LYS cc_start: 0.7305 (mppt) cc_final: 0.6808 (mppt) REVERT: G 75 TYR cc_start: 0.9110 (m-80) cc_final: 0.8869 (m-80) REVERT: G 106 PHE cc_start: 0.8924 (m-80) cc_final: 0.8505 (m-80) REVERT: H 56 CYS cc_start: 0.7079 (p) cc_final: 0.6727 (p) REVERT: I 116 ARG cc_start: 0.3496 (mpt180) cc_final: 0.1987 (tpp-160) REVERT: I 276 LYS cc_start: 0.2775 (tttt) cc_final: 0.2522 (tttt) REVERT: K 85 ARG cc_start: 0.5549 (OUTLIER) cc_final: 0.4781 (ptm160) REVERT: Q 163 LYS cc_start: 0.8951 (ptpp) cc_final: 0.8558 (ptpp) outliers start: 101 outliers final: 73 residues processed: 195 average time/residue: 0.1712 time to fit residues: 54.6495 Evaluate side-chains 183 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 104 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 PHE Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 94 HIS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 207 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 258 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.081151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.054766 restraints weight = 133761.658| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.47 r_work: 0.3252 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29572 Z= 0.213 Angle : 0.845 14.592 41470 Z= 0.383 Chirality : 0.073 1.403 4840 Planarity : 0.004 0.062 4076 Dihedral : 19.744 178.068 6842 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.42 % Allowed : 25.88 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2649 helix: 0.99 (0.13), residues: 1553 sheet: -1.20 (0.34), residues: 229 loop : -1.12 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 128 TYR 0.025 0.002 TYR H 73 PHE 0.015 0.002 PHE H 106 TRP 0.016 0.001 TRP J 45 HIS 0.009 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (29564) covalent geometry : angle 0.84489 / 0.38 (41461) hydrogen bonds : bond 0.04141 / 2.75 ( 1455) hydrogen bonds : angle 4.08795 / 2.92 ( 3996) metal coordination : bond 0.00828 / 0.44 ( 8) metal coordination : angle 2.21943 / 1.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 112 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8161 (t0) REVERT: A 513 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: E 196 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7111 (t80) REVERT: E 231 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8190 (mmp-170) REVERT: F 17 ASP cc_start: 0.6005 (OUTLIER) cc_final: 0.5509 (p0) REVERT: F 131 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: F 147 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: F 204 PHE cc_start: 0.8560 (m-80) cc_final: 0.8283 (m-80) REVERT: G 75 TYR cc_start: 0.9109 (m-80) cc_final: 0.8885 (m-80) REVERT: G 98 GLN cc_start: 0.8294 (tp40) cc_final: 0.7828 (tp40) REVERT: G 106 PHE cc_start: 0.8848 (m-80) cc_final: 0.8475 (m-80) REVERT: H 73 TYR cc_start: 0.6322 (t80) cc_final: 0.5999 (t80) REVERT: I 116 ARG cc_start: 0.3466 (mpt180) cc_final: 0.2164 (tpp-160) REVERT: I 147 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: K 85 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4754 (ptm160) REVERT: Q 163 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8497 (ptpp) REVERT: X 14 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8060 (pp20) outliers start: 99 outliers final: 71 residues processed: 197 average time/residue: 0.1641 time to fit residues: 53.1314 Evaluate side-chains 189 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 108 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 PHE Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 94 HIS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 14 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 109 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 224 optimal weight: 30.0000 chunk 289 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.080399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.056630 restraints weight = 134798.968| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.58 r_work: 0.3192 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29572 Z= 0.287 Angle : 0.906 15.407 41470 Z= 0.411 Chirality : 0.076 1.409 4840 Planarity : 0.005 0.070 4076 Dihedral : 19.768 179.207 6842 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.46 % Allowed : 26.10 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2649 helix: 0.82 (0.13), residues: 1552 sheet: -1.21 (0.34), residues: 229 loop : -1.21 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 128 TYR 0.025 0.002 TYR H 73 PHE 0.017 0.002 PHE A 567 TRP 0.018 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.29 (29564) covalent geometry : angle 0.90554 / 0.41 (41461) hydrogen bonds : bond 0.04738 / 3.14 ( 1455) hydrogen bonds : angle 4.17176 / 2.98 ( 3996) metal coordination : bond 0.00998 / 0.55 ( 8) metal coordination : angle 2.49726 / 1.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 110 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8228 (t0) REVERT: A 513 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: A 606 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8522 (mm) REVERT: E 196 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7279 (t80) REVERT: F 17 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.5777 (p0) REVERT: F 131 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: F 147 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: F 204 PHE cc_start: 0.8578 (m-10) cc_final: 0.8345 (m-80) REVERT: F 276 LYS cc_start: 0.7317 (mppt) cc_final: 0.7094 (mptt) REVERT: G 98 GLN cc_start: 0.8249 (tp40) cc_final: 0.7797 (tp40) REVERT: I 61 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: I 116 ARG cc_start: 0.3465 (mpt180) cc_final: 0.2095 (tpp-160) REVERT: I 147 ASP cc_start: 0.6484 (OUTLIER) cc_final: 0.6133 (m-30) REVERT: K 85 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.4793 (ptm160) REVERT: Q 163 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8521 (ptpp) REVERT: X 14 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8132 (pp20) outliers start: 100 outliers final: 78 residues processed: 198 average time/residue: 0.1654 time to fit residues: 53.4249 Evaluate side-chains 195 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 106 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 PHE Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 94 HIS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 14 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 204 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 196 optimal weight: 40.0000 chunk 80 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.082118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.055910 restraints weight = 134486.269| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.63 r_work: 0.3294 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29572 Z= 0.140 Angle : 0.800 12.687 41470 Z= 0.364 Chirality : 0.070 1.406 4840 Planarity : 0.004 0.056 4076 Dihedral : 19.682 178.566 6842 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.17 % Allowed : 27.26 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2649 helix: 1.15 (0.13), residues: 1553 sheet: -1.14 (0.34), residues: 229 loop : -1.05 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 128 TYR 0.022 0.001 TYR H 73 PHE 0.019 0.001 PHE G 106 TRP 0.017 0.002 TRP E 45 HIS 0.008 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (29564) covalent geometry : angle 0.79932 / 0.36 (41461) hydrogen bonds : bond 0.03693 / 2.44 ( 1455) hydrogen bonds : angle 3.99604 / 2.87 ( 3996) metal coordination : bond 0.00587 / 0.31 ( 8) metal coordination : angle 2.00079 / 1.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 114 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8042 (t0) REVERT: A 513 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: A 606 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8493 (mm) REVERT: E 196 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6985 (t80) REVERT: E 210 MET cc_start: 0.7170 (tmm) cc_final: 0.6922 (tmm) REVERT: E 231 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8208 (mmp-170) REVERT: F 17 ASP cc_start: 0.6036 (OUTLIER) cc_final: 0.5540 (p0) REVERT: F 131 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: F 147 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: F 204 PHE cc_start: 0.8555 (m-10) cc_final: 0.8301 (m-80) REVERT: F 276 LYS cc_start: 0.7245 (mppt) cc_final: 0.6973 (mptt) REVERT: G 98 GLN cc_start: 0.8243 (tp40) cc_final: 0.7797 (tp40) REVERT: G 106 PHE cc_start: 0.8875 (m-80) cc_final: 0.8562 (m-80) REVERT: H 73 TYR cc_start: 0.6428 (t80) cc_final: 0.6098 (t80) REVERT: I 116 ARG cc_start: 0.3451 (mpt180) cc_final: 0.2222 (tpp-160) REVERT: I 147 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.5872 (m-30) REVERT: K 85 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.4806 (ptm160) REVERT: Q 142 MET cc_start: 0.8305 (mmp) cc_final: 0.8096 (mmt) REVERT: Q 163 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8533 (ptpp) REVERT: X 14 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8096 (pp20) outliers start: 71 outliers final: 46 residues processed: 174 average time/residue: 0.1652 time to fit residues: 46.0434 Evaluate side-chains 166 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 185 optimal weight: 8.9990 chunk 268 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.081826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.055513 restraints weight = 133422.478| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.61 r_work: 0.3281 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29572 Z= 0.165 Angle : 0.801 13.879 41470 Z= 0.365 Chirality : 0.069 1.392 4840 Planarity : 0.004 0.064 4076 Dihedral : 19.623 179.656 6842 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.77 % Allowed : 27.58 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2649 helix: 1.21 (0.13), residues: 1553 sheet: -1.14 (0.34), residues: 229 loop : -0.99 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 148 TYR 0.022 0.001 TYR H 73 PHE 0.014 0.001 PHE H 106 TRP 0.015 0.001 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (29564) covalent geometry : angle 0.80035 / 0.37 (41461) hydrogen bonds : bond 0.03831 / 2.54 ( 1455) hydrogen bonds : angle 3.96831 / 2.84 ( 3996) metal coordination : bond 0.00584 / 0.32 ( 8) metal coordination : angle 2.17850 / 1.30 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8076 (t0) REVERT: A 513 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: A 606 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8498 (mm) REVERT: E 196 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7049 (t80) REVERT: E 210 MET cc_start: 0.7119 (tmm) cc_final: 0.6881 (tmm) REVERT: E 231 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8187 (mmp-170) REVERT: F 17 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5514 (p0) REVERT: F 131 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: F 147 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: F 204 PHE cc_start: 0.8580 (m-10) cc_final: 0.8321 (m-80) REVERT: G 98 GLN cc_start: 0.8194 (tp40) cc_final: 0.7761 (tp40) REVERT: G 106 PHE cc_start: 0.8869 (m-80) cc_final: 0.8492 (m-80) REVERT: H 73 TYR cc_start: 0.6409 (t80) cc_final: 0.6082 (t80) REVERT: I 116 ARG cc_start: 0.3454 (mpt180) cc_final: 0.2233 (tpp-160) REVERT: I 147 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.5935 (m-30) REVERT: K 85 ARG cc_start: 0.5614 (OUTLIER) cc_final: 0.4904 (ptm160) REVERT: Q 163 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8468 (ptpp) outliers start: 62 outliers final: 47 residues processed: 165 average time/residue: 0.1737 time to fit residues: 45.8611 Evaluate side-chains 169 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 112 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 296 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 147 optimal weight: 40.0000 chunk 127 optimal weight: 0.0000 chunk 93 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 chunk 180 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.081724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.055573 restraints weight = 133716.101| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.60 r_work: 0.3273 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29572 Z= 0.178 Angle : 0.809 12.742 41470 Z= 0.369 Chirality : 0.069 1.380 4840 Planarity : 0.004 0.060 4076 Dihedral : 19.603 178.949 6842 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.08 % Allowed : 27.44 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2649 helix: 1.20 (0.13), residues: 1559 sheet: -1.11 (0.34), residues: 229 loop : -1.00 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 128 TYR 0.023 0.001 TYR H 73 PHE 0.014 0.001 PHE G 106 TRP 0.013 0.001 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (29564) covalent geometry : angle 0.80822 / 0.37 (41461) hydrogen bonds : bond 0.03852 / 2.55 ( 1455) hydrogen bonds : angle 3.94781 / 2.82 ( 3996) metal coordination : bond 0.00636 / 0.34 ( 8) metal coordination : angle 2.20616 / 1.33 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9903.91 seconds wall clock time: 169 minutes 33.95 seconds (10173.95 seconds total)