Starting phenix.real_space_refine on Sun Jul 5 13:53:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bd5_15975/07_2026/8bd5_15975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd5_15975/07_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_15975/07_2026/8bd5_15975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd5_15975/07_2026/8bd5_15975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bd5_15975/07_2026/8bd5_15975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd5_15975/07_2026/8bd5_15975.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bd5_15975/07_2026/8bd5_15975.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bd5_15975/07_2026/8bd5_15975.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 246} Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 106, 'rna3p_pyr': 102} Link IDs: {'rna2p': 38, 'rna3p': 207} 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: 6.59, per 1000 atoms: 0.23 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 953.2 milliseconds 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: 3.77 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: 6.03 Time building geometry restraints manager: 3.70 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: 40350 1.81 - 3.62: 994 3.62 - 5.44: 96 5.44 - 7.25: 16 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=" 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 angle pdb=" O4' DC C -18 " pdb=" C1' DC C -18 " pdb=" N1 DC C -18 " ideal model delta sigma weight residual 108.00 111.14 -3.14 7.00e-01 2.04e+00 2.02e+01 ... (remaining 41456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 16081 35.96 - 71.93: 1076 71.93 - 107.89: 60 107.89 - 143.86: 6 143.86 - 179.82: 12 Dihedral angle restraints: 17235 sinusoidal: 9476 harmonic: 7759 Sorted by residual: dihedral pdb=" O4' U B 23 " pdb=" C1' U B 23 " pdb=" N1 U B 23 " pdb=" C2 U B 23 " ideal model delta sinusoidal sigma weight residual -128.00 51.03 -179.03 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 129 " pdb=" C1' U B 129 " pdb=" N1 U B 129 " pdb=" C2 U B 129 " ideal model delta sinusoidal sigma weight residual 232.00 54.85 177.15 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 138 " pdb=" C1' U B 138 " pdb=" N1 U B 138 " pdb=" C2 U B 138 " ideal model delta sinusoidal sigma weight residual 232.00 54.94 177.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 17232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3691 0.042 - 0.085: 835 0.085 - 0.127: 279 0.127 - 0.169: 28 0.169 - 0.211: 7 Chirality restraints: 4840 Sorted by residual: chirality pdb=" C3' G B 15 " pdb=" C4' G B 15 " pdb=" O3' G B 15 " pdb=" C2' G B 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C3' DC D 6 " pdb=" C4' DC D 6 " pdb=" O3' DC D 6 " pdb=" C2' DC D 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.83e-01 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 2.41 -2.61 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (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: 10.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.400 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- 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= 0.270 Angle : 0.658 19.395 41470 Z= 0.424 Chirality : 0.041 0.211 4840 Planarity : 0.004 0.096 4076 Dihedral : 20.492 179.825 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 0.00406 / 0.27 (29564) covalent geometry : angle 0.64704 / 0.42 (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 : 0.891 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: 0.1942 time to fit residues: 35.4336 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 : 0.811 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.081846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.058177 restraints weight = 135009.189| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.26 r_work: 0.3239 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29572 Z= 0.187 Angle : 0.610 8.163 41470 Z= 0.329 Chirality : 0.042 0.376 4840 Planarity : 0.005 0.072 4076 Dihedral : 19.173 178.016 6858 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 26.15 % Favored : 71.31 % 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: 0.15 (0.16), residues: 2649 helix: 1.02 (0.13), residues: 1549 sheet: -1.65 (0.42), residues: 143 loop : -1.08 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 243 TYR 0.022 0.002 TYR H 73 PHE 0.018 0.002 PHE H 106 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 0.00383 / 0.19 (29564) covalent geometry : angle 0.60865 / 0.33 (41461) hydrogen bonds : bond 0.04583 / 3.01 ( 1455) hydrogen bonds : angle 4.45044 / 3.19 ( 3996) metal coordination : bond 0.00848 / 0.45 ( 8) metal coordination : angle 2.42067 / 1.53 ( 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 159 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8085 (t0) REVERT: F 147 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: G 98 GLN cc_start: 0.8271 (tp40) cc_final: 0.7896 (tp40) REVERT: G 149 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7329 (pp) REVERT: G 205 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6974 (pttt) REVERT: H 73 TYR cc_start: 0.6369 (t80) cc_final: 0.6086 (t80) REVERT: I 108 LYS cc_start: 0.7368 (mtpt) cc_final: 0.7005 (mtpp) outliers start: 57 outliers final: 25 residues processed: 151 average time/residue: 0.1842 time to fit residues: 45.6125 Evaluate side-chains 125 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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: 4.9990 chunk 281 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 279 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 264 optimal weight: 0.0170 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 200 optimal weight: 50.0000 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.082533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058091 restraints weight = 134264.469| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.24 r_work: 0.3285 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 29572 Z= 0.127 Angle : 0.551 7.504 41470 Z= 0.297 Chirality : 0.039 0.393 4840 Planarity : 0.004 0.059 4076 Dihedral : 19.026 179.279 6842 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.63 % Allowed : 25.66 % Favored : 71.71 % 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: 0.43 (0.16), residues: 2649 helix: 1.24 (0.13), residues: 1549 sheet: -1.62 (0.41), residues: 141 loop : -0.95 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 243 TYR 0.016 0.001 TYR H 73 PHE 0.015 0.001 PHE J 204 TRP 0.015 0.001 TRP G 45 HIS 0.008 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (29564) covalent geometry : angle 0.54966 / 0.30 (41461) hydrogen bonds : bond 0.03910 / 2.56 ( 1455) hydrogen bonds : angle 4.12902 / 2.95 ( 3996) metal coordination : bond 0.00566 / 0.31 ( 8) metal coordination : angle 2.20017 / 1.31 ( 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 175 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8030 (t0) REVERT: F 275 TYR cc_start: 0.7209 (t80) cc_final: 0.6892 (t80) REVERT: G 75 TYR cc_start: 0.9088 (m-80) cc_final: 0.8659 (m-80) REVERT: G 98 GLN cc_start: 0.8265 (tp40) cc_final: 0.7876 (tp40) REVERT: G 106 PHE cc_start: 0.8908 (m-80) cc_final: 0.8592 (m-80) REVERT: H 56 CYS cc_start: 0.6874 (p) cc_final: 0.6602 (p) REVERT: H 73 TYR cc_start: 0.6437 (t80) cc_final: 0.6151 (t80) REVERT: H 275 TYR cc_start: 0.1190 (m-80) cc_final: 0.0928 (m-80) REVERT: I 80 GLN cc_start: 0.3268 (OUTLIER) cc_final: 0.2983 (pm20) REVERT: I 116 ARG cc_start: 0.3500 (mpt180) cc_final: 0.1999 (tpp-160) outliers start: 59 outliers final: 28 residues processed: 165 average time/residue: 0.1904 time to fit residues: 50.9121 Evaluate side-chains 132 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 39 VAL 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 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: 6.9990 chunk 90 optimal weight: 40.0000 chunk 13 optimal weight: 30.0000 chunk 109 optimal weight: 40.0000 chunk 261 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** A 603 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.080888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.056890 restraints weight = 134430.678| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.29 r_work: 0.3206 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 29572 Z= 0.280 Angle : 0.654 8.954 41470 Z= 0.348 Chirality : 0.044 0.395 4840 Planarity : 0.005 0.055 4076 Dihedral : 19.010 179.355 6842 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.02 % Allowed : 25.39 % Favored : 70.59 % 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: 0.09 (0.16), residues: 2649 helix: 0.96 (0.13), residues: 1553 sheet: -1.19 (0.34), residues: 230 loop : -1.14 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 243 TYR 0.046 0.002 TYR K 75 PHE 0.020 0.002 PHE A 567 TRP 0.014 0.002 TRP J 45 HIS 0.009 0.002 HIS Q 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.28 (29564) covalent geometry : angle 0.65296 / 0.35 (41461) hydrogen bonds : bond 0.04847 / 3.20 ( 1455) hydrogen bonds : angle 4.21048 / 3.01 ( 3996) metal coordination : bond 0.00982 / 0.55 ( 8) metal coordination : angle 2.71742 / 1.74 ( 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 194 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 104 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 513 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: F 103 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8476 (tttp) REVERT: F 131 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: F 147 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: G 75 TYR cc_start: 0.9091 (m-80) cc_final: 0.8819 (m-80) REVERT: G 106 PHE cc_start: 0.8956 (m-80) cc_final: 0.8531 (m-80) REVERT: G 149 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7364 (pp) REVERT: G 205 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.7008 (pttt) REVERT: H 56 CYS cc_start: 0.6986 (p) cc_final: 0.6498 (p) REVERT: H 190 PHE cc_start: 0.5653 (m-10) cc_final: 0.5437 (m-10) REVERT: H 275 TYR cc_start: 0.1199 (m-80) cc_final: 0.0937 (m-80) REVERT: I 116 ARG cc_start: 0.3470 (mpt180) cc_final: 0.1975 (tpp-160) REVERT: K 75 TYR cc_start: 0.7454 (m-80) cc_final: 0.7160 (m-80) REVERT: Q 8 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8349 (ttpt) outliers start: 90 outliers final: 54 residues processed: 183 average time/residue: 0.2048 time to fit residues: 59.3100 Evaluate side-chains 162 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 101 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 103 LYS 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 85 ARG Chi-restraints excluded: chain G residue 138 VAL 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 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 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 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 34 VAL 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 204 PHE Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 21 SER 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: 0.0670 chunk 104 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 290 optimal weight: 7.9990 chunk 223 optimal weight: 40.0000 chunk 202 optimal weight: 0.0170 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4177 r_free = 0.4177 target = 0.082699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.058175 restraints weight = 134106.634| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.30 r_work: 0.3287 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29572 Z= 0.115 Angle : 0.550 11.677 41470 Z= 0.293 Chirality : 0.039 0.395 4840 Planarity : 0.004 0.051 4076 Dihedral : 18.960 178.205 6842 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.95 % Allowed : 26.06 % Favored : 71.00 % 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: 0.48 (0.17), residues: 2649 helix: 1.29 (0.13), residues: 1552 sheet: -1.14 (0.33), residues: 230 loop : -0.97 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 128 TYR 0.038 0.001 TYR K 75 PHE 0.022 0.001 PHE H 106 TRP 0.015 0.001 TRP E 45 HIS 0.009 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (29564) covalent geometry : angle 0.54899 / 0.29 (41461) hydrogen bonds : bond 0.03646 / 2.37 ( 1455) hydrogen bonds : angle 3.96653 / 2.84 ( 3996) metal coordination : bond 0.00488 / 0.27 ( 8) metal coordination : angle 2.04314 / 1.19 ( 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 179 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 113 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8070 (t0) REVERT: A 513 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: F 131 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: F 147 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: F 275 TYR cc_start: 0.7282 (t80) cc_final: 0.6988 (t80) REVERT: G 75 TYR cc_start: 0.9113 (m-80) cc_final: 0.8816 (m-80) REVERT: G 85 ARG cc_start: 0.5538 (OUTLIER) cc_final: 0.5295 (ttp-170) REVERT: G 98 GLN cc_start: 0.8263 (tp40) cc_final: 0.7866 (tp40) REVERT: G 106 PHE cc_start: 0.8911 (m-80) cc_final: 0.8578 (m-80) REVERT: G 205 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.7013 (pttt) REVERT: H 56 CYS cc_start: 0.7025 (p) cc_final: 0.6587 (p) REVERT: H 275 TYR cc_start: 0.1112 (m-80) cc_final: 0.0873 (m-80) REVERT: I 80 GLN cc_start: 0.3234 (OUTLIER) cc_final: 0.2962 (pm20) REVERT: I 116 ARG cc_start: 0.3503 (mpt180) cc_final: 0.2051 (tpp-160) REVERT: J 34 VAL cc_start: 0.3484 (OUTLIER) cc_final: 0.3209 (t) REVERT: K 75 TYR cc_start: 0.7519 (m-80) cc_final: 0.7223 (m-80) outliers start: 66 outliers final: 35 residues processed: 168 average time/residue: 0.1947 time to fit residues: 52.7792 Evaluate side-chains 150 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 355 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS 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 246 GLU 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 176 LEU 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 85 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 205 LYS 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 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 K residue 39 VAL Chi-restraints excluded: chain K residue 173 THR 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: 0.7980 chunk 158 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 164 optimal weight: 0.0870 chunk 265 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.1764 ------------------------------------------------------------------------------- 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 ** H 43 HIS ** 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 = 0.4156 r_free = 0.4156 target = 0.081853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.056970 restraints weight = 134070.304| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.52 r_work: 0.3261 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29572 Z= 0.179 Angle : 0.561 10.985 41470 Z= 0.301 Chirality : 0.040 0.396 4840 Planarity : 0.004 0.054 4076 Dihedral : 18.875 179.641 6842 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.53 % Allowed : 25.79 % Favored : 70.68 % 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: 0.48 (0.17), residues: 2649 helix: 1.27 (0.13), residues: 1554 sheet: -1.16 (0.33), residues: 230 loop : -0.93 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.033 0.002 TYR K 75 PHE 0.018 0.001 PHE H 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 0.00367 / 0.18 (29564) covalent geometry : angle 0.56050 / 0.30 (41461) hydrogen bonds : bond 0.03931 / 2.58 ( 1455) hydrogen bonds : angle 3.92680 / 2.81 ( 3996) metal coordination : bond 0.00660 / 0.37 ( 8) metal coordination : angle 2.25201 / 1.37 ( 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 186 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 107 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7993 (t0) REVERT: A 513 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: E 231 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (mmp-170) REVERT: F 103 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8317 (tttp) REVERT: F 131 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: F 147 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: G 75 TYR cc_start: 0.9114 (m-80) cc_final: 0.8858 (m-80) REVERT: G 85 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.5281 (ttp-170) REVERT: G 106 PHE cc_start: 0.8919 (m-80) cc_final: 0.8559 (m-80) REVERT: G 205 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6989 (pttt) REVERT: H 275 TYR cc_start: 0.1104 (m-80) cc_final: 0.0866 (m-80) REVERT: I 80 GLN cc_start: 0.3175 (OUTLIER) cc_final: 0.2916 (pm20) REVERT: I 116 ARG cc_start: 0.3491 (mpt180) cc_final: 0.2044 (tpp-160) REVERT: J 34 VAL cc_start: 0.3555 (OUTLIER) cc_final: 0.3339 (t) REVERT: K 75 TYR cc_start: 0.7527 (m-80) cc_final: 0.7244 (m-80) REVERT: K 85 ARG cc_start: 0.5549 (OUTLIER) cc_final: 0.4779 (ptm160) REVERT: K 212 GLU cc_start: 0.4367 (OUTLIER) cc_final: 0.3765 (mt-10) outliers start: 79 outliers final: 45 residues processed: 177 average time/residue: 0.2056 time to fit residues: 58.4403 Evaluate side-chains 163 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 355 VAL Chi-restraints excluded: chain A residue 383 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 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 103 LYS 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 85 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 205 LYS 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 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 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 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 212 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 207 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 overall best weight: 2.1982 ------------------------------------------------------------------------------- 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 98 GLN Q 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.082194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.058220 restraints weight = 133568.206| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.38 r_work: 0.3263 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29572 Z= 0.143 Angle : 0.551 10.631 41470 Z= 0.295 Chirality : 0.039 0.397 4840 Planarity : 0.004 0.050 4076 Dihedral : 18.861 179.565 6842 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.26 % Allowed : 26.06 % Favored : 70.68 % 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: 0.53 (0.17), residues: 2649 helix: 1.30 (0.13), residues: 1560 sheet: -1.13 (0.33), residues: 230 loop : -0.91 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 128 TYR 0.031 0.001 TYR K 75 PHE 0.028 0.001 PHE H 106 TRP 0.014 0.001 TRP A 21 HIS 0.007 0.001 HIS K 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (29564) covalent geometry : angle 0.55068 / 0.29 (41461) hydrogen bonds : bond 0.03703 / 2.42 ( 1455) hydrogen bonds : angle 3.88598 / 2.78 ( 3996) metal coordination : bond 0.00581 / 0.32 ( 8) metal coordination : angle 2.11525 / 1.26 ( 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 188 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 115 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: E 231 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8192 (mmp-170) REVERT: F 131 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: F 147 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: F 204 PHE cc_start: 0.8574 (m-80) cc_final: 0.8267 (m-80) REVERT: F 275 TYR cc_start: 0.7366 (t80) cc_final: 0.7108 (t80) REVERT: G 75 TYR cc_start: 0.9106 (m-80) cc_final: 0.8843 (m-80) REVERT: G 85 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5200 (ttp-170) REVERT: G 98 GLN cc_start: 0.8245 (tp40) cc_final: 0.7815 (tp40) REVERT: G 106 PHE cc_start: 0.8910 (m-80) cc_final: 0.8551 (m-80) REVERT: G 205 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.7002 (pttt) REVERT: H 73 TYR cc_start: 0.6211 (t80) cc_final: 0.5908 (t80) REVERT: H 275 TYR cc_start: 0.1033 (m-80) cc_final: 0.0788 (m-80) REVERT: I 80 GLN cc_start: 0.3103 (OUTLIER) cc_final: 0.2841 (pm20) REVERT: I 116 ARG cc_start: 0.3468 (mpt180) cc_final: 0.2022 (tpp-160) REVERT: I 147 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: J 34 VAL cc_start: 0.3471 (OUTLIER) cc_final: 0.3253 (t) REVERT: K 75 TYR cc_start: 0.7575 (m-80) cc_final: 0.7290 (m-80) REVERT: K 85 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.4835 (ptm160) REVERT: K 212 GLU cc_start: 0.4307 (OUTLIER) cc_final: 0.3680 (mt-10) REVERT: K 262 LYS cc_start: 0.0900 (OUTLIER) cc_final: 0.0625 (mmmt) outliers start: 73 outliers final: 49 residues processed: 179 average time/residue: 0.1949 time to fit residues: 56.0949 Evaluate side-chains 172 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 111 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 355 VAL Chi-restraints excluded: chain A residue 383 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 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 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 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 85 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 210 MET 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 80 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 232 ILE 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 85 ARG Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 262 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 109 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 224 optimal weight: 30.0000 chunk 289 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 296 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.081117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.056435 restraints weight = 134009.306| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.35 r_work: 0.3206 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29572 Z= 0.213 Angle : 0.597 10.378 41470 Z= 0.318 Chirality : 0.041 0.398 4840 Planarity : 0.004 0.057 4076 Dihedral : 18.831 178.319 6842 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.70 % Allowed : 25.75 % Favored : 70.55 % 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: 0.38 (0.17), residues: 2649 helix: 1.16 (0.13), residues: 1560 sheet: -1.12 (0.34), residues: 230 loop : -0.95 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 126 TYR 0.030 0.002 TYR K 75 PHE 0.021 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 0.00442 / 0.21 (29564) covalent geometry : angle 0.59561 / 0.32 (41461) hydrogen bonds : bond 0.04210 / 2.77 ( 1455) hydrogen bonds : angle 3.95871 / 2.83 ( 3996) metal coordination : bond 0.00789 / 0.43 ( 8) metal coordination : angle 2.43524 / 1.51 ( 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 192 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 109 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 513 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: F 131 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: F 147 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: F 204 PHE cc_start: 0.8604 (m-80) cc_final: 0.8289 (m-80) REVERT: G 75 TYR cc_start: 0.9109 (m-80) cc_final: 0.8866 (m-80) REVERT: G 85 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.5358 (ttp-170) REVERT: G 106 PHE cc_start: 0.8897 (m-80) cc_final: 0.8499 (m-80) REVERT: G 205 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6987 (pttt) REVERT: H 275 TYR cc_start: 0.1159 (m-80) cc_final: 0.0950 (m-80) REVERT: I 80 GLN cc_start: 0.3032 (OUTLIER) cc_final: 0.2761 (pm20) REVERT: I 116 ARG cc_start: 0.3491 (mpt180) cc_final: 0.2097 (tpp-160) REVERT: I 147 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: J 34 VAL cc_start: 0.3498 (OUTLIER) cc_final: 0.3273 (t) REVERT: K 75 TYR cc_start: 0.7569 (m-80) cc_final: 0.7306 (m-80) REVERT: K 85 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.4836 (ptm160) REVERT: K 212 GLU cc_start: 0.4325 (OUTLIER) cc_final: 0.3755 (mt-10) outliers start: 83 outliers final: 54 residues processed: 183 average time/residue: 0.1887 time to fit residues: 56.1780 Evaluate side-chains 172 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 107 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 54 LEU 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 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 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 A residue 575 GLN 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 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 36 LEU Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 117 VAL 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 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 80 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 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 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 212 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 204 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 overall best weight: 4.5590 ------------------------------------------------------------------------------- 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** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN ** 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 = 0.4137 r_free = 0.4137 target = 0.081114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.056467 restraints weight = 134591.335| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.24 r_work: 0.3220 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29572 Z= 0.225 Angle : 0.618 11.011 41470 Z= 0.329 Chirality : 0.042 0.401 4840 Planarity : 0.004 0.055 4076 Dihedral : 18.843 177.717 6842 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.57 % Allowed : 26.06 % Favored : 70.37 % 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: 0.26 (0.16), residues: 2649 helix: 1.06 (0.13), residues: 1559 sheet: -1.12 (0.34), residues: 230 loop : -0.99 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 133 TYR 0.030 0.002 TYR K 75 PHE 0.020 0.002 PHE H 106 TRP 0.015 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (29564) covalent geometry : angle 0.61753 / 0.33 (41461) hydrogen bonds : bond 0.04269 / 2.82 ( 1455) hydrogen bonds : angle 4.00881 / 2.86 ( 3996) metal coordination : bond 0.00888 / 0.49 ( 8) metal coordination : angle 2.33649 / 1.47 ( 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 191 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 111 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8135 (t0) REVERT: A 513 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: A 606 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8513 (mm) REVERT: E 231 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8175 (mmp-170) REVERT: F 131 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: F 147 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: F 204 PHE cc_start: 0.8629 (m-80) cc_final: 0.8345 (m-80) REVERT: G 75 TYR cc_start: 0.9110 (m-80) cc_final: 0.8870 (m-80) REVERT: G 149 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7177 (pp) REVERT: G 205 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.7008 (pttt) REVERT: H 73 TYR cc_start: 0.6228 (t80) cc_final: 0.5920 (t80) REVERT: I 80 GLN cc_start: 0.3038 (OUTLIER) cc_final: 0.2759 (pm20) REVERT: I 116 ARG cc_start: 0.3458 (mpt180) cc_final: 0.2060 (tpp-160) REVERT: I 147 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: K 75 TYR cc_start: 0.7519 (m-80) cc_final: 0.7276 (m-80) REVERT: K 85 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.4879 (ptm160) REVERT: K 212 GLU cc_start: 0.4576 (OUTLIER) cc_final: 0.3972 (mt-10) outliers start: 80 outliers final: 59 residues processed: 182 average time/residue: 0.1877 time to fit residues: 55.6604 Evaluate side-chains 179 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 108 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 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 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 A residue 575 GLN 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 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 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 36 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL 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 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 80 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 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 212 GLU Chi-restraints excluded: chain K residue 275 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 185 optimal weight: 7.9990 chunk 268 optimal weight: 50.0000 chunk 169 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.081542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056627 restraints weight = 132666.593| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.09 r_work: 0.3240 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29572 Z= 0.155 Angle : 0.570 9.742 41470 Z= 0.304 Chirality : 0.040 0.400 4840 Planarity : 0.004 0.054 4076 Dihedral : 18.798 179.970 6842 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.08 % Allowed : 26.64 % Favored : 70.28 % 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: 0.44 (0.17), residues: 2649 helix: 1.21 (0.13), residues: 1559 sheet: -1.11 (0.34), residues: 230 loop : -0.93 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 148 TYR 0.029 0.002 TYR K 75 PHE 0.020 0.001 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 0.00317 / 0.16 (29564) covalent geometry : angle 0.56891 / 0.30 (41461) hydrogen bonds : bond 0.03806 / 2.49 ( 1455) hydrogen bonds : angle 3.90275 / 2.79 ( 3996) metal coordination : bond 0.00639 / 0.35 ( 8) metal coordination : angle 2.06092 / 1.23 ( 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 184 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 115 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 513 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: A 606 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8498 (mm) REVERT: E 231 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8200 (mmp-170) REVERT: F 103 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8299 (tttp) REVERT: F 131 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: F 147 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: F 204 PHE cc_start: 0.8649 (m-80) cc_final: 0.8386 (m-80) REVERT: F 275 TYR cc_start: 0.7420 (t80) cc_final: 0.7154 (t80) REVERT: G 75 TYR cc_start: 0.9114 (m-80) cc_final: 0.8864 (m-80) REVERT: G 106 PHE cc_start: 0.8909 (m-80) cc_final: 0.8617 (m-80) REVERT: H 73 TYR cc_start: 0.6272 (t80) cc_final: 0.5942 (t80) REVERT: I 80 GLN cc_start: 0.2986 (OUTLIER) cc_final: 0.2703 (pm20) REVERT: I 116 ARG cc_start: 0.3444 (mpt180) cc_final: 0.2072 (tpp-160) REVERT: I 147 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: K 75 TYR cc_start: 0.7519 (m-80) cc_final: 0.7294 (m-80) REVERT: K 85 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.4939 (ptm160) REVERT: K 212 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.3862 (mt-10) outliers start: 69 outliers final: 51 residues processed: 176 average time/residue: 0.1990 time to fit residues: 56.1630 Evaluate side-chains 175 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 113 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 68 THR 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 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 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 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 103 LYS 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 36 LEU Chi-restraints excluded: chain G residue 117 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 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 80 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 232 ILE 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 212 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 68 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 296 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** ** 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 = 0.4135 r_free = 0.4135 target = 0.081029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.056578 restraints weight = 134167.847| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.31 r_work: 0.3217 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29572 Z= 0.240 Angle : 0.628 9.971 41470 Z= 0.333 Chirality : 0.043 0.403 4840 Planarity : 0.004 0.058 4076 Dihedral : 18.815 178.020 6842 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.12 % Allowed : 26.51 % Favored : 70.37 % 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: 0.24 (0.16), residues: 2649 helix: 1.03 (0.13), residues: 1559 sheet: -1.13 (0.34), residues: 230 loop : -0.99 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 126 TYR 0.028 0.002 TYR K 75 PHE 0.018 0.002 PHE H 106 TRP 0.015 0.002 TRP J 45 HIS 0.007 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (29564) covalent geometry : angle 0.62724 / 0.33 (41461) hydrogen bonds : bond 0.04429 / 2.92 ( 1455) hydrogen bonds : angle 4.00614 / 2.86 ( 3996) metal coordination : bond 0.00901 / 0.49 ( 8) metal coordination : angle 2.49417 / 1.56 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10398.28 seconds wall clock time: 178 minutes 7.35 seconds (10687.35 seconds total)