Starting phenix.real_space_refine on Mon Aug 25 13:31:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bd5_15975/08_2025/8bd5_15975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd5_15975/08_2025/8bd5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2025/8bd5_15975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2025/8bd5_15975.map" model { file = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2025/8bd5_15975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd5_15975/08_2025/8bd5_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.76, per 1000 atoms: 0.20 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: 2.36 Conformation dependent library (CDL) restraints added in 692.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.59 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: 4.77 Time building geometry restraints manager: 3.11 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=" 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 bond pdb=" N VAL I 68 " pdb=" CA VAL I 68 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.52e+00 bond pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.43e+00 ... (remaining 29559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 40494 1.81 - 3.62: 858 3.62 - 5.44: 88 5.44 - 7.25: 16 7.25 - 9.06: 5 Bond angle restraints: 41461 Sorted by residual: angle pdb=" N ASN Q 59 " pdb=" CA ASN Q 59 " pdb=" C ASN Q 59 " ideal model delta sigma weight residual 113.25 107.53 5.72 1.30e+00 5.92e-01 1.94e+01 angle pdb=" N ASP H 147 " pdb=" CA ASP H 147 " pdb=" C ASP H 147 " ideal model delta sigma weight residual 112.72 107.83 4.89 1.14e+00 7.69e-01 1.84e+01 angle pdb=" N ASP F 147 " pdb=" CA ASP F 147 " pdb=" C ASP F 147 " ideal model delta sigma weight residual 113.02 108.03 4.99 1.20e+00 6.94e-01 1.73e+01 angle pdb=" CA GLN F 213 " pdb=" CB GLN F 213 " pdb=" CG GLN F 213 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" N PRO Q 60 " pdb=" CA PRO Q 60 " pdb=" C PRO Q 60 " ideal model delta sigma weight residual 112.47 104.62 7.85 2.06e+00 2.36e-01 1.45e+01 ... (remaining 41456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 16598 35.96 - 71.93: 1576 71.93 - 107.89: 118 107.89 - 143.86: 6 143.86 - 179.82: 12 Dihedral angle restraints: 18310 sinusoidal: 10551 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 18307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3742 0.042 - 0.085: 818 0.085 - 0.127: 251 0.127 - 0.169: 23 0.169 - 0.211: 6 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=" 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 chirality pdb=" CB ILE I 142 " pdb=" CA ILE I 142 " pdb=" CG1 ILE I 142 " pdb=" CG2 ILE I 142 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.33e-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: 6.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 27.490 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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= 0.199 Angle : 0.635 19.395 41470 Z= 0.355 Chirality : 0.040 0.211 4840 Planarity : 0.004 0.096 4076 Dihedral : 23.072 179.825 13282 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 aren 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 covalent geometry : bond 0.00380 (29564) covalent geometry : angle 0.62288 (41461) hydrogen bonds : bond 0.12553 ( 1455) hydrogen bonds : angle 5.61562 ( 3996) metal coordination : bond 0.05872 ( 8) metal coordination : angle 8.24840 ( 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 : 0.922 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: 0.1669 time to fit residues: 30.6657 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 : 0.867 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4154 r_free = 0.4154 target = 0.081827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.056468 restraints weight = 134770.951| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.11 r_work: 0.3260 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29572 Z= 0.191 Angle : 0.593 8.149 41470 Z= 0.317 Chirality : 0.039 0.193 4840 Planarity : 0.005 0.072 4076 Dihedral : 23.379 179.541 7933 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.63 % Allowed : 25.93 % Favored : 71.44 % 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 aren not related in a simple way. whole: 0.20 (0.16), residues: 2649 helix: 1.06 (0.13), residues: 1549 sheet: -1.66 (0.42), residues: 143 loop : -1.07 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 243 TYR 0.021 0.002 TYR H 73 PHE 0.019 0.002 PHE H 106 TRP 0.013 0.001 TRP G 45 HIS 0.009 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00406 (29564) covalent geometry : angle 0.59148 (41461) hydrogen bonds : bond 0.04491 ( 1455) hydrogen bonds : angle 4.38004 ( 3996) metal coordination : bond 0.00813 ( 8) metal coordination : angle 2.51986 ( 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 162 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 103 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8112 (t0) REVERT: F 147 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: G 98 GLN cc_start: 0.8269 (tp40) cc_final: 0.7888 (tp40) REVERT: G 106 PHE cc_start: 0.8914 (m-80) cc_final: 0.8545 (m-80) REVERT: G 149 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7273 (pp) REVERT: H 73 TYR cc_start: 0.6402 (t80) cc_final: 0.6111 (t80) REVERT: I 80 GLN cc_start: 0.3368 (OUTLIER) cc_final: 0.3048 (pm20) REVERT: K 214 MET cc_start: 0.4535 (mmm) cc_final: 0.3675 (ptm) outliers start: 59 outliers final: 26 residues processed: 154 average time/residue: 0.1862 time to fit residues: 47.3130 Evaluate side-chains 129 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 355 VAL Chi-restraints excluded: chain A residue 383 THR 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 25 ILE 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 121 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 97 HIS 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 34 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 24 optimal weight: 5.9990 chunk 281 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 200 optimal weight: 40.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4154 r_free = 0.4154 target = 0.081797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.058233 restraints weight = 134651.298| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.64 r_work: 0.3238 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29572 Z= 0.181 Angle : 0.570 7.247 41470 Z= 0.305 Chirality : 0.039 0.193 4840 Planarity : 0.004 0.062 4076 Dihedral : 23.174 179.989 7919 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.84 % Allowed : 25.03 % Favored : 71.13 % 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 aren not related in a simple way. whole: 0.32 (0.16), residues: 2649 helix: 1.16 (0.13), residues: 1549 sheet: -1.67 (0.42), residues: 143 loop : -0.99 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 243 TYR 0.027 0.002 TYR K 75 PHE 0.016 0.001 PHE G 204 TRP 0.013 0.001 TRP J 45 HIS 0.009 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00385 (29564) covalent geometry : angle 0.56895 (41461) hydrogen bonds : bond 0.04130 ( 1455) hydrogen bonds : angle 4.12568 ( 3996) metal coordination : bond 0.00750 ( 8) metal coordination : angle 2.43533 ( 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 197 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 111 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8098 (t0) REVERT: A 513 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: F 103 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8351 (tttp) REVERT: F 131 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: G 75 TYR cc_start: 0.9079 (m-80) cc_final: 0.8691 (m-80) REVERT: G 98 GLN cc_start: 0.8299 (tp40) cc_final: 0.7890 (tp40) REVERT: G 106 PHE cc_start: 0.8921 (m-80) cc_final: 0.8538 (m-80) REVERT: G 149 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7409 (pp) REVERT: H 56 CYS cc_start: 0.6791 (p) cc_final: 0.6488 (p) REVERT: H 94 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7607 (mp) REVERT: H 142 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7734 (tp) REVERT: H 275 TYR cc_start: 0.1103 (m-80) cc_final: 0.0872 (m-80) REVERT: I 116 ARG cc_start: 0.3601 (mpt180) cc_final: 0.1995 (tpp-160) REVERT: K 214 MET cc_start: 0.4433 (mmm) cc_final: 0.3441 (ptm) REVERT: Q 163 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8553 (ptpp) outliers start: 86 outliers final: 41 residues processed: 185 average time/residue: 0.2009 time to fit residues: 59.6344 Evaluate side-chains 149 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 21 LEU 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 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 210 MET Chi-restraints excluded: chain H residue 94 ILE 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 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 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 39 VAL Chi-restraints excluded: chain K residue 122 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 199 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 6.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 213 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.080426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.056441 restraints weight = 134559.125| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.27 r_work: 0.3178 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 29572 Z= 0.309 Angle : 0.678 8.016 41470 Z= 0.359 Chirality : 0.044 0.205 4840 Planarity : 0.005 0.062 4076 Dihedral : 23.161 177.586 7919 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.00 % Allowed : 25.35 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 2649 helix: 0.78 (0.13), residues: 1552 sheet: -1.14 (0.34), residues: 230 loop : -1.22 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.025 0.002 TYR A 91 PHE 0.031 0.002 PHE H 106 TRP 0.019 0.002 TRP G 45 HIS 0.009 0.002 HIS Q 34 Details of bonding type rmsd covalent geometry : bond 0.00663 (29564) covalent geometry : angle 0.67718 (41461) hydrogen bonds : bond 0.05106 ( 1455) hydrogen bonds : angle 4.26695 ( 3996) metal coordination : bond 0.01120 ( 8) metal coordination : angle 2.75973 ( 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 220 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 108 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8441 (t70) REVERT: E 196 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7352 (t80) REVERT: F 103 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8505 (tttp) REVERT: F 131 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: F 147 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: G 75 TYR cc_start: 0.9069 (m-80) cc_final: 0.8823 (m-80) REVERT: G 149 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7379 (pp) REVERT: H 56 CYS cc_start: 0.7027 (p) cc_final: 0.6445 (p) REVERT: H 190 PHE cc_start: 0.5878 (m-10) cc_final: 0.5653 (m-10) REVERT: H 275 TYR cc_start: 0.1168 (m-80) cc_final: 0.0966 (m-80) REVERT: K 212 GLU cc_start: 0.4595 (OUTLIER) cc_final: 0.3929 (mt-10) REVERT: K 214 MET cc_start: 0.4433 (mmm) cc_final: 0.3450 (ptm) REVERT: Q 163 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8531 (ptpp) outliers start: 112 outliers final: 60 residues processed: 207 average time/residue: 0.2019 time to fit residues: 66.9516 Evaluate side-chains 170 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 103 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 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 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 147 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 103 LYS 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 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 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 21 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 98 optimal weight: 0.0970 chunk 104 optimal weight: 7.9990 chunk 243 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 223 optimal weight: 30.0000 chunk 202 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.081825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.058704 restraints weight = 134613.488| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.03 r_work: 0.3254 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29572 Z= 0.156 Angle : 0.558 9.571 41470 Z= 0.298 Chirality : 0.038 0.193 4840 Planarity : 0.004 0.057 4076 Dihedral : 23.049 179.867 7919 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.61 % Allowed : 26.28 % Favored : 70.10 % 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 aren not related in a simple way. whole: 0.27 (0.16), residues: 2649 helix: 1.11 (0.13), residues: 1557 sheet: -1.09 (0.34), residues: 230 loop : -1.09 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 254 TYR 0.022 0.001 TYR H 73 PHE 0.021 0.001 PHE H 106 TRP 0.015 0.001 TRP J 45 HIS 0.008 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00331 (29564) covalent geometry : angle 0.55737 (41461) hydrogen bonds : bond 0.03819 ( 1455) hydrogen bonds : angle 3.98370 ( 3996) metal coordination : bond 0.00706 ( 8) metal coordination : angle 2.22917 ( 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 200 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 119 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8050 (t0) REVERT: A 513 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: E 196 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7024 (t80) REVERT: F 131 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: F 147 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: F 204 PHE cc_start: 0.8546 (m-80) cc_final: 0.8234 (m-80) REVERT: F 276 LYS cc_start: 0.7194 (mppt) cc_final: 0.6943 (mptt) REVERT: G 75 TYR cc_start: 0.9120 (m-80) cc_final: 0.8851 (m-80) REVERT: G 85 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.5297 (ttp-170) REVERT: G 106 PHE cc_start: 0.8881 (m-80) cc_final: 0.8551 (m-80) REVERT: H 56 CYS cc_start: 0.7107 (p) cc_final: 0.6631 (p) REVERT: H 73 TYR cc_start: 0.6391 (t80) cc_final: 0.6079 (t80) REVERT: I 80 GLN cc_start: 0.3137 (OUTLIER) cc_final: 0.2857 (pm20) REVERT: I 116 ARG cc_start: 0.3605 (mpt180) cc_final: 0.2080 (tpp-160) REVERT: I 147 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6146 (m-30) REVERT: K 212 GLU cc_start: 0.4477 (OUTLIER) cc_final: 0.3865 (mt-10) REVERT: K 214 MET cc_start: 0.4343 (mmm) cc_final: 0.3465 (ptm) REVERT: Q 163 LYS cc_start: 0.8937 (ptpp) cc_final: 0.8546 (ptpp) outliers start: 81 outliers final: 42 residues processed: 190 average time/residue: 0.1972 time to fit residues: 60.5440 Evaluate side-chains 163 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 301 LEU 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 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 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 196 PHE 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 38 GLN Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 212 GLU 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: 5.9990 chunk 158 optimal weight: 5.9990 chunk 195 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.081171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.056522 restraints weight = 134210.332| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.23 r_work: 0.3224 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29572 Z= 0.203 Angle : 0.584 13.227 41470 Z= 0.310 Chirality : 0.039 0.196 4840 Planarity : 0.004 0.055 4076 Dihedral : 22.976 179.305 7919 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.37 % Allowed : 25.66 % Favored : 69.97 % 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 aren not related in a simple way. whole: 0.26 (0.16), residues: 2649 helix: 1.09 (0.13), residues: 1557 sheet: -1.11 (0.34), residues: 230 loop : -1.07 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 254 TYR 0.020 0.002 TYR A 91 PHE 0.016 0.002 PHE H 106 TRP 0.016 0.001 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00435 (29564) covalent geometry : angle 0.58351 (41461) hydrogen bonds : bond 0.04132 ( 1455) hydrogen bonds : angle 3.97511 ( 3996) metal coordination : bond 0.00758 ( 8) metal coordination : angle 2.33230 ( 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 211 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 113 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 513 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: E 196 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7097 (t80) REVERT: F 81 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7189 (tp40) REVERT: F 103 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8310 (tttp) REVERT: F 131 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: F 147 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: F 204 PHE cc_start: 0.8579 (m-10) cc_final: 0.8309 (m-80) REVERT: G 75 TYR cc_start: 0.9105 (m-80) cc_final: 0.8863 (m-80) REVERT: G 85 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.5281 (ttp-170) REVERT: G 106 PHE cc_start: 0.8856 (m-80) cc_final: 0.8474 (m-80) REVERT: H 56 CYS cc_start: 0.7207 (p) cc_final: 0.6883 (p) REVERT: I 61 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: I 80 GLN cc_start: 0.3168 (OUTLIER) cc_final: 0.2875 (pm20) REVERT: I 116 ARG cc_start: 0.3579 (mpt180) cc_final: 0.2081 (tpp-160) REVERT: I 147 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: K 85 ARG cc_start: 0.5729 (OUTLIER) cc_final: 0.4908 (ptm160) REVERT: K 212 GLU cc_start: 0.4558 (OUTLIER) cc_final: 0.3950 (mt-10) REVERT: K 214 MET cc_start: 0.4359 (mmm) cc_final: 0.3521 (ptm) REVERT: Q 163 LYS cc_start: 0.8913 (ptpp) cc_final: 0.8487 (ptpp) outliers start: 98 outliers final: 57 residues processed: 201 average time/residue: 0.1971 time to fit residues: 64.0042 Evaluate side-chains 180 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 110 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 383 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG 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 81 GLN Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 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 196 PHE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 61 GLU 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 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL 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 13 LEU 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: 9.9990 chunk 67 optimal weight: 10.0000 chunk 124 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.081523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057281 restraints weight = 133017.520| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.19 r_work: 0.3226 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29572 Z= 0.159 Angle : 0.559 13.034 41470 Z= 0.296 Chirality : 0.038 0.193 4840 Planarity : 0.004 0.055 4076 Dihedral : 22.903 179.335 7919 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.24 % Allowed : 26.15 % Favored : 69.61 % 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 aren not related in a simple way. whole: 0.39 (0.17), residues: 2649 helix: 1.19 (0.13), residues: 1557 sheet: -1.12 (0.33), residues: 230 loop : -0.98 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 128 TYR 0.023 0.001 TYR H 73 PHE 0.016 0.001 PHE H 106 TRP 0.015 0.001 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00338 (29564) covalent geometry : angle 0.55830 (41461) hydrogen bonds : bond 0.03732 ( 1455) hydrogen bonds : angle 3.90540 ( 3996) metal coordination : bond 0.00631 ( 8) metal coordination : angle 2.24624 ( 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 210 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 115 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7557 (t) REVERT: A 513 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: A 606 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8504 (mm) REVERT: E 196 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6958 (t80) REVERT: E 231 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8148 (mmp-170) REVERT: F 81 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7287 (tp40) REVERT: F 131 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: F 147 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: F 204 PHE cc_start: 0.8580 (m-10) cc_final: 0.8307 (m-10) REVERT: G 75 TYR cc_start: 0.9114 (m-80) cc_final: 0.8880 (m-80) REVERT: G 85 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.5148 (ttp-170) REVERT: G 106 PHE cc_start: 0.8863 (m-80) cc_final: 0.8587 (m-80) REVERT: H 56 CYS cc_start: 0.7242 (p) cc_final: 0.6982 (p) REVERT: H 73 TYR cc_start: 0.6345 (t80) cc_final: 0.5929 (t80) REVERT: I 80 GLN cc_start: 0.3043 (OUTLIER) cc_final: 0.2761 (pm20) REVERT: I 116 ARG cc_start: 0.3589 (mpt180) cc_final: 0.2149 (tpp-160) REVERT: I 147 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6202 (m-30) REVERT: K 85 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.4903 (ptm160) REVERT: K 212 GLU cc_start: 0.4397 (OUTLIER) cc_final: 0.3741 (mt-10) REVERT: Q 163 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8512 (ptpp) outliers start: 95 outliers final: 58 residues processed: 199 average time/residue: 0.2021 time to fit residues: 64.2633 Evaluate side-chains 182 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 111 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 CYS 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 A residue 555 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL 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 81 GLN Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 85 ARG 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 113 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 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 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 94 HIS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 109 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 224 optimal weight: 30.0000 chunk 289 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 296 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.080784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.055885 restraints weight = 134195.424| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.97 r_work: 0.3220 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29572 Z= 0.222 Angle : 0.606 12.594 41470 Z= 0.319 Chirality : 0.040 0.196 4840 Planarity : 0.004 0.059 4076 Dihedral : 22.881 179.199 7919 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.11 % Allowed : 26.51 % Favored : 69.39 % 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 aren not related in a simple way. whole: 0.27 (0.16), residues: 2649 helix: 1.06 (0.13), residues: 1570 sheet: -1.26 (0.35), residues: 203 loop : -0.98 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 128 TYR 0.023 0.002 TYR H 73 PHE 0.016 0.002 PHE A 567 TRP 0.016 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00477 (29564) covalent geometry : angle 0.60471 (41461) hydrogen bonds : bond 0.04194 ( 1455) hydrogen bonds : angle 3.97037 ( 3996) metal coordination : bond 0.00837 ( 8) metal coordination : angle 2.36200 ( 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 207 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 115 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8059 (t0) REVERT: A 412 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7581 (t) REVERT: A 513 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: A 606 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8525 (mm) REVERT: E 196 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7142 (t80) REVERT: E 231 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8243 (mmp-170) REVERT: F 81 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7180 (tp40) REVERT: F 131 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: F 147 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: F 204 PHE cc_start: 0.8576 (m-10) cc_final: 0.8290 (m-80) REVERT: G 75 TYR cc_start: 0.9111 (m-80) cc_final: 0.8875 (m-80) REVERT: G 106 PHE cc_start: 0.8831 (m-80) cc_final: 0.8537 (m-80) REVERT: I 61 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: I 80 GLN cc_start: 0.3050 (OUTLIER) cc_final: 0.2759 (pm20) REVERT: I 116 ARG cc_start: 0.3543 (mpt180) cc_final: 0.2142 (tpp-160) REVERT: I 147 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6183 (m-30) REVERT: K 85 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.4919 (ptm160) REVERT: K 212 GLU cc_start: 0.4393 (OUTLIER) cc_final: 0.3768 (mt-10) REVERT: Q 163 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8517 (ptpp) outliers start: 92 outliers final: 65 residues processed: 196 average time/residue: 0.2015 time to fit residues: 63.4942 Evaluate side-chains 191 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 112 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 ASP 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 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 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 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 113 LEU 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 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 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 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL 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 97 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 15 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 196 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 overall best weight: 3.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.080908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.056442 restraints weight = 134506.811| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.19 r_work: 0.3205 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29572 Z= 0.209 Angle : 0.599 12.178 41470 Z= 0.316 Chirality : 0.040 0.196 4840 Planarity : 0.004 0.057 4076 Dihedral : 22.858 179.935 7919 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.97 % Allowed : 26.60 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.16), residues: 2649 helix: 1.06 (0.13), residues: 1568 sheet: -1.25 (0.35), residues: 203 loop : -1.01 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 128 TYR 0.027 0.002 TYR H 73 PHE 0.015 0.002 PHE A 567 TRP 0.018 0.001 TRP J 45 HIS 0.007 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00447 (29564) covalent geometry : angle 0.59846 (41461) hydrogen bonds : bond 0.04071 ( 1455) hydrogen bonds : angle 3.97293 ( 3996) metal coordination : bond 0.00833 ( 8) metal coordination : angle 2.35926 ( 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 201 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 112 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.7603 (t) REVERT: A 513 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: A 606 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8536 (mm) REVERT: E 196 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7170 (t80) REVERT: E 231 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8249 (mmp-170) REVERT: F 81 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7149 (tp40) REVERT: F 103 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8383 (tttp) REVERT: F 131 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: F 147 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: F 204 PHE cc_start: 0.8567 (m-10) cc_final: 0.8222 (m-80) REVERT: G 75 TYR cc_start: 0.9108 (m-80) cc_final: 0.8892 (m-80) REVERT: G 85 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.5387 (ttp-170) REVERT: G 106 PHE cc_start: 0.8834 (m-80) cc_final: 0.8553 (m-80) REVERT: H 73 TYR cc_start: 0.6289 (t80) cc_final: 0.5937 (t80) REVERT: H 275 TYR cc_start: 0.1552 (m-80) cc_final: 0.1276 (m-80) REVERT: I 61 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: I 80 GLN cc_start: 0.2981 (OUTLIER) cc_final: 0.2704 (pm20) REVERT: I 116 ARG cc_start: 0.3446 (mpt180) cc_final: 0.2106 (tpp-160) REVERT: I 147 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6266 (m-30) REVERT: K 85 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.4954 (ptm160) REVERT: K 212 GLU cc_start: 0.4360 (OUTLIER) cc_final: 0.3726 (mt-10) REVERT: Q 163 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8531 (ptpp) outliers start: 89 outliers final: 67 residues processed: 191 average time/residue: 0.1990 time to fit residues: 60.8277 Evaluate side-chains 192 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 110 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 118 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 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 555 VAL 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 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 113 LEU 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 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 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 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL 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 97 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 15 LYS 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: 30.0000 chunk 268 optimal weight: 0.0060 chunk 169 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4172 r_free = 0.4172 target = 0.082477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058005 restraints weight = 133229.752| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.30 r_work: 0.3281 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29572 Z= 0.118 Angle : 0.560 16.116 41470 Z= 0.294 Chirality : 0.037 0.188 4840 Planarity : 0.004 0.052 4076 Dihedral : 22.732 178.115 7919 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 27.93 % Favored : 69.52 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2649 helix: 1.30 (0.13), residues: 1570 sheet: -1.16 (0.35), residues: 203 loop : -0.86 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 128 TYR 0.022 0.001 TYR H 73 PHE 0.015 0.001 PHE H 106 TRP 0.027 0.002 TRP K 211 HIS 0.006 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00247 (29564) covalent geometry : angle 0.55930 (41461) hydrogen bonds : bond 0.03455 ( 1455) hydrogen bonds : angle 3.82391 ( 3996) metal coordination : bond 0.00362 ( 8) metal coordination : angle 2.23299 ( 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 179 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: A 606 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8485 (mm) REVERT: E 196 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7087 (t80) REVERT: E 231 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7956 (mmp80) REVERT: F 81 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7226 (tp40) REVERT: F 147 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: F 204 PHE cc_start: 0.8563 (m-10) cc_final: 0.8289 (m-10) REVERT: G 75 TYR cc_start: 0.9100 (m-80) cc_final: 0.8865 (m-80) REVERT: G 98 GLN cc_start: 0.8248 (tp40) cc_final: 0.7797 (tp40) REVERT: G 106 PHE cc_start: 0.8860 (m-80) cc_final: 0.8625 (m-80) REVERT: H 56 CYS cc_start: 0.7147 (p) cc_final: 0.6583 (p) REVERT: H 73 TYR cc_start: 0.6295 (t80) cc_final: 0.5967 (t80) REVERT: H 112 TYR cc_start: 0.5274 (t80) cc_final: 0.4996 (t80) REVERT: H 275 TYR cc_start: 0.1555 (m-80) cc_final: 0.1318 (m-80) REVERT: I 61 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: I 116 ARG cc_start: 0.3421 (mpt180) cc_final: 0.2093 (tpp-160) REVERT: I 147 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: K 85 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5086 (ptm160) REVERT: K 212 GLU cc_start: 0.4469 (OUTLIER) cc_final: 0.3838 (mt-10) REVERT: Q 163 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8525 (ptpp) outliers start: 57 outliers final: 36 residues processed: 173 average time/residue: 0.2022 time to fit residues: 55.7322 Evaluate side-chains 159 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 355 VAL 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 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 81 GLN Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP 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 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 113 LEU 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 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain Q residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 68 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4158 r_free = 0.4158 target = 0.081902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.058422 restraints weight = 134283.153| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.34 r_work: 0.3256 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29572 Z= 0.151 Angle : 0.564 12.384 41470 Z= 0.297 Chirality : 0.038 0.191 4840 Planarity : 0.004 0.057 4076 Dihedral : 22.657 179.962 7919 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.72 % Allowed : 27.80 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2649 helix: 1.37 (0.13), residues: 1561 sheet: -0.94 (0.34), residues: 230 loop : -0.91 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 148 TYR 0.022 0.001 TYR H 73 PHE 0.016 0.001 PHE H 106 TRP 0.017 0.001 TRP K 211 HIS 0.006 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00321 (29564) covalent geometry : angle 0.56311 (41461) hydrogen bonds : bond 0.03648 ( 1455) hydrogen bonds : angle 3.82035 ( 3996) metal coordination : bond 0.00516 ( 8) metal coordination : angle 2.25993 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10783.02 seconds wall clock time: 184 minutes 43.66 seconds (11083.66 seconds total)