Starting phenix.real_space_refine on Tue Jun 24 10:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bd5_15975/06_2025/8bd5_15975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd5_15975/06_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_15975/06_2025/8bd5_15975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd5_15975/06_2025/8bd5_15975.map" model { file = "/net/cci-nas-00/data/ceres_data/8bd5_15975/06_2025/8bd5_15975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd5_15975/06_2025/8bd5_15975.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: 18.99, per 1000 atoms: 0.67 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: 7.21 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 154 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 136 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 151 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 133 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 125 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 103 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 100 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 122 " Number of angles added : 9 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5028 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 13 sheets defined 63.4% alpha, 5.7% beta 118 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 11.38 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: 14.71 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5624 1.33 - 1.45: 8100 1.45 - 1.57: 15030 1.57 - 1.69: 684 1.69 - 1.81: 126 Bond restraints: 29564 Sorted by residual: bond pdb=" N PRO I 79 " pdb=" CD PRO I 79 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" 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 276 \ or resid 301 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 276 or resid 301 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 276 \ or resid 301 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 276 \ or resid 301 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 276 \ or resid 301 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 276 or resid 301 th \ rough 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 276 \ or resid 301 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: 1131.920 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: 0.030 Extract box with map and model: 1.310 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 80.520 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1218.680 ------------------------------------------------------------------------------- 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 : 16.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.013 0.002 TRP J 45 HIS 0.005 0.001 HIS A 586 PHE 0.013 0.001 PHE F 204 TYR 0.024 0.002 TYR H 73 ARG 0.005 0.000 ARG I 128 Details of bonding type rmsd hydrogen bonds : bond 0.12553 ( 1455) hydrogen bonds : angle 5.61562 ( 3996) metal coordination : bond 0.05872 ( 8) metal coordination : angle 8.24840 ( 9) covalent geometry : bond 0.00380 (29564) covalent geometry : angle 0.62288 (41461) *********************** 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 : 3.150 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: 0.4616 time to fit residues: 84.3705 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 : 2.683 ------------------------------------------------------------------------------- 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 251 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 270 optimal weight: 40.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 E 98 GLN F 37 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN Q 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.080229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.057012 restraints weight = 134560.829| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.29 r_work: 0.3183 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 29572 Z= 0.354 Angle : 0.724 7.738 41470 Z= 0.383 Chirality : 0.046 0.230 4840 Planarity : 0.006 0.076 4076 Dihedral : 23.433 178.756 7933 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.33 % Allowed : 25.30 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2649 helix: 0.66 (0.13), residues: 1550 sheet: -1.15 (0.33), residues: 245 loop : -1.39 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 45 HIS 0.011 0.002 HIS F 77 PHE 0.021 0.002 PHE A 567 TYR 0.026 0.002 TYR A 91 ARG 0.009 0.001 ARG G 243 Details of bonding type rmsd hydrogen bonds : bond 0.05560 ( 1455) hydrogen bonds : angle 4.57985 ( 3996) metal coordination : bond 0.01414 ( 8) metal coordination : angle 2.79009 ( 9) covalent geometry : bond 0.00757 (29564) covalent geometry : angle 0.72250 (41461) *********************** 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 202 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 105 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8479 (t70) REVERT: A 513 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 551 MET cc_start: 0.8782 (tpp) cc_final: 0.8438 (tpt) REVERT: F 103 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8476 (tttp) REVERT: F 196 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: G 149 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7367 (pp) REVERT: G 152 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: G 205 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6979 (pttt) REVERT: H 45 TRP cc_start: 0.3714 (OUTLIER) cc_final: 0.3244 (t60) REVERT: K 75 TYR cc_start: 0.7306 (m-10) cc_final: 0.7106 (m-80) REVERT: K 214 MET cc_start: 0.4555 (mmm) cc_final: 0.3657 (ptm) outliers start: 97 outliers final: 46 residues processed: 189 average time/residue: 0.3881 time to fit residues: 119.6948 Evaluate side-chains 154 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 66 LEU 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 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 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 583 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 196 PHE 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 149 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 45 TRP Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain 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 122 VAL Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 292 optimal weight: 0.9990 chunk 284 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 200 optimal weight: 40.0000 chunk 51 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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** Q 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.082364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.055993 restraints weight = 133620.799| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.55 r_work: 0.3299 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29572 Z= 0.126 Angle : 0.557 8.011 41470 Z= 0.297 Chirality : 0.038 0.191 4840 Planarity : 0.004 0.061 4076 Dihedral : 23.228 179.256 7921 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.44 % Allowed : 26.10 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2649 helix: 1.13 (0.13), residues: 1551 sheet: -1.08 (0.33), residues: 245 loop : -1.17 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 45 HIS 0.009 0.001 HIS F 77 PHE 0.014 0.001 PHE J 204 TYR 0.018 0.001 TYR H 73 ARG 0.005 0.000 ARG I 128 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1455) hydrogen bonds : angle 4.14386 ( 3996) metal coordination : bond 0.00665 ( 8) metal coordination : angle 2.34614 ( 9) covalent geometry : bond 0.00262 (29564) covalent geometry : angle 0.55635 (41461) *********************** 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 194 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 117 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8075 (t0) REVERT: A 551 MET cc_start: 0.8530 (tpp) cc_final: 0.8205 (tpt) REVERT: F 131 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: F 276 LYS cc_start: 0.7117 (mppt) cc_final: 0.6658 (mppt) REVERT: G 75 TYR cc_start: 0.9092 (m-80) cc_final: 0.8749 (m-80) REVERT: G 98 GLN cc_start: 0.8262 (tp40) cc_final: 0.7892 (tp40) REVERT: G 106 PHE cc_start: 0.8889 (m-80) cc_final: 0.8561 (m-80) REVERT: H 45 TRP cc_start: 0.3741 (OUTLIER) cc_final: 0.3329 (t60) REVERT: I 80 GLN cc_start: 0.3208 (OUTLIER) cc_final: 0.2966 (pm20) REVERT: I 116 ARG cc_start: 0.3550 (mpt180) cc_final: 0.2172 (tpp-160) REVERT: K 214 MET cc_start: 0.4247 (mmm) cc_final: 0.3456 (ptm) REVERT: Q 163 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8583 (ptpp) outliers start: 77 outliers final: 32 residues processed: 182 average time/residue: 0.5128 time to fit residues: 146.9694 Evaluate side-chains 140 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 3.362 ------------------------------------------------------------------------------- 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 303 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET 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 45 TRP Chi-restraints excluded: chain H residue 143 ILE 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 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 281 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 162 optimal weight: 0.2980 chunk 110 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.081639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.057136 restraints weight = 134608.933| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.23 r_work: 0.3246 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1233 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= 0.186 Angle : 0.573 9.145 41470 Z= 0.305 Chirality : 0.039 0.194 4840 Planarity : 0.004 0.057 4076 Dihedral : 23.096 179.475 7921 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.02 % Allowed : 25.70 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2649 helix: 1.14 (0.13), residues: 1553 sheet: -1.15 (0.34), residues: 230 loop : -1.08 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 45 HIS 0.008 0.001 HIS F 77 PHE 0.013 0.001 PHE A 567 TYR 0.021 0.002 TYR H 73 ARG 0.006 0.000 ARG I 128 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 1455) hydrogen bonds : angle 4.05555 ( 3996) metal coordination : bond 0.00701 ( 8) metal coordination : angle 2.38623 ( 9) covalent geometry : bond 0.00399 (29564) covalent geometry : angle 0.57238 (41461) *********************** 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 199 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 109 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8096 (t0) REVERT: E 196 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7658 (t80) REVERT: F 131 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: G 75 TYR cc_start: 0.9097 (m-80) cc_final: 0.8814 (m-80) REVERT: G 98 GLN cc_start: 0.8226 (tp40) cc_final: 0.7818 (tp40) REVERT: G 106 PHE cc_start: 0.8902 (m-80) cc_final: 0.8538 (m-80) REVERT: G 205 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.7046 (pttt) REVERT: H 45 TRP cc_start: 0.3678 (OUTLIER) cc_final: 0.3168 (t60) REVERT: I 80 GLN cc_start: 0.3250 (OUTLIER) cc_final: 0.2949 (pm20) REVERT: I 116 ARG cc_start: 0.3583 (mpt180) cc_final: 0.2081 (tpp-160) REVERT: K 212 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.3887 (mt-10) REVERT: K 214 MET cc_start: 0.4344 (mmm) cc_final: 0.3500 (ptm) REVERT: Q 163 LYS cc_start: 0.8883 (ptpp) cc_final: 0.8528 (ptpp) outliers start: 90 outliers final: 43 residues processed: 190 average time/residue: 0.5481 time to fit residues: 173.7116 Evaluate side-chains 150 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 6.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR 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 607 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain H residue 45 TRP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 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 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 20.0000 chunk 53 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- 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 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.081456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.057076 restraints weight = 134001.258| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.28 r_work: 0.3234 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1449 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= 0.191 Angle : 0.578 13.736 41470 Z= 0.306 Chirality : 0.039 0.195 4840 Planarity : 0.004 0.054 4076 Dihedral : 23.010 179.921 7921 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.60 % Allowed : 25.08 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2649 helix: 1.13 (0.13), residues: 1554 sheet: -1.18 (0.33), residues: 230 loop : -1.04 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 45 HIS 0.008 0.001 HIS F 77 PHE 0.025 0.002 PHE H 106 TYR 0.027 0.002 TYR K 75 ARG 0.005 0.000 ARG I 128 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1455) hydrogen bonds : angle 3.99944 ( 3996) metal coordination : bond 0.00765 ( 8) metal coordination : angle 2.47485 ( 9) covalent geometry : bond 0.00409 (29564) covalent geometry : angle 0.57685 (41461) *********************** 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 217 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 114 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8122 (t0) REVERT: A 232 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 513 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: E 196 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7130 (t80) REVERT: E 231 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8180 (mmp-170) REVERT: F 103 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8279 (tttp) REVERT: F 131 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: F 204 PHE cc_start: 0.8557 (m-80) cc_final: 0.8158 (m-80) REVERT: F 276 LYS cc_start: 0.7102 (mppt) cc_final: 0.6843 (mptt) REVERT: G 75 TYR cc_start: 0.9116 (m-80) cc_final: 0.8861 (m-80) REVERT: G 106 PHE cc_start: 0.8881 (m-80) cc_final: 0.8522 (m-80) REVERT: G 149 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7241 (pp) REVERT: H 45 TRP cc_start: 0.3692 (OUTLIER) cc_final: 0.3141 (t60) REVERT: I 80 GLN cc_start: 0.3149 (OUTLIER) cc_final: 0.2861 (pm20) REVERT: I 116 ARG cc_start: 0.3516 (mpt180) cc_final: 0.2089 (tpp-160) REVERT: I 147 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6262 (m-30) REVERT: K 212 GLU cc_start: 0.4550 (OUTLIER) cc_final: 0.3888 (mt-10) REVERT: K 214 MET cc_start: 0.4435 (mmm) cc_final: 0.3554 (ptm) REVERT: Q 163 LYS cc_start: 0.8905 (ptpp) cc_final: 0.8496 (ptpp) outliers start: 103 outliers final: 59 residues processed: 206 average time/residue: 0.5582 time to fit residues: 192.1952 Evaluate side-chains 181 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 110 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU 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 389 ILE 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 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 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 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 LEU 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 45 TRP 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 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 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 122 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain Q residue 94 HIS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 103 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 272 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 149 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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** I 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.081023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.056287 restraints weight = 134676.411| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.21 r_work: 0.3224 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29572 Z= 0.224 Angle : 0.604 12.050 41470 Z= 0.320 Chirality : 0.040 0.197 4840 Planarity : 0.004 0.060 4076 Dihedral : 22.982 179.292 7921 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.33 % Allowed : 26.10 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2649 helix: 1.06 (0.13), residues: 1554 sheet: -1.20 (0.33), residues: 230 loop : -1.05 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 45 HIS 0.008 0.001 HIS F 77 PHE 0.015 0.002 PHE A 567 TYR 0.025 0.002 TYR H 73 ARG 0.005 0.000 ARG I 128 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 1455) hydrogen bonds : angle 4.02601 ( 3996) metal coordination : bond 0.00871 ( 8) metal coordination : angle 2.41104 ( 9) covalent geometry : bond 0.00480 (29564) covalent geometry : angle 0.60292 (41461) *********************** 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: 97 poor density : 114 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8080 (t0) REVERT: A 513 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: A 606 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8524 (mm) REVERT: E 196 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7234 (t80) REVERT: F 81 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7217 (tp40) REVERT: F 131 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: F 204 PHE cc_start: 0.8568 (m-10) cc_final: 0.8299 (m-80) REVERT: F 276 LYS cc_start: 0.7181 (mppt) cc_final: 0.6658 (mppt) REVERT: G 75 TYR cc_start: 0.9101 (m-80) cc_final: 0.8896 (m-80) REVERT: G 106 PHE cc_start: 0.8863 (m-80) cc_final: 0.8482 (m-80) REVERT: G 149 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7189 (pp) REVERT: H 45 TRP cc_start: 0.3668 (OUTLIER) cc_final: 0.3092 (t60) REVERT: I 61 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: I 116 ARG cc_start: 0.3534 (mpt180) cc_final: 0.2102 (tpp-160) REVERT: I 147 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: K 85 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.4906 (ptm160) REVERT: K 212 GLU cc_start: 0.4419 (OUTLIER) cc_final: 0.3778 (mt-10) REVERT: K 214 MET cc_start: 0.4502 (mmm) cc_final: 0.4302 (mtt) REVERT: Q 163 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8506 (ptpp) outliers start: 97 outliers final: 68 residues processed: 201 average time/residue: 0.5747 time to fit residues: 188.5754 Evaluate side-chains 191 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 111 time to evaluate : 2.977 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 SER 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 389 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 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 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 131 GLU 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 85 ARG Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 LEU 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 45 TRP 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 210 MET Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 87 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 188 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.080496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.055688 restraints weight = 134253.618| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.25 r_work: 0.3209 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29572 Z= 0.270 Angle : 0.648 11.770 41470 Z= 0.343 Chirality : 0.042 0.200 4840 Planarity : 0.005 0.061 4076 Dihedral : 23.012 178.590 7921 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.18 % Allowed : 25.57 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2649 helix: 0.81 (0.13), residues: 1569 sheet: -1.42 (0.35), residues: 203 loop : -1.06 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 PHE 0.017 0.002 PHE A 567 TYR 0.029 0.002 TYR H 73 ARG 0.006 0.001 ARG G 243 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1455) hydrogen bonds : angle 4.14500 ( 3996) metal coordination : bond 0.01074 ( 8) metal coordination : angle 2.59188 ( 9) covalent geometry : bond 0.00579 (29564) covalent geometry : angle 0.64712 (41461) *********************** 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 233 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 117 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 513 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: A 606 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8518 (mm) REVERT: E 196 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7172 (t80) REVERT: E 210 MET cc_start: 0.7216 (tmm) cc_final: 0.7005 (tmm) REVERT: E 231 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8249 (mmp-170) REVERT: F 103 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8415 (tttp) REVERT: F 131 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: F 204 PHE cc_start: 0.8524 (m-10) cc_final: 0.8285 (m-10) REVERT: G 106 PHE cc_start: 0.8814 (m-80) cc_final: 0.8486 (m-80) REVERT: G 149 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7169 (pp) REVERT: H 45 TRP cc_start: 0.3690 (OUTLIER) cc_final: 0.3055 (t60) REVERT: I 61 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: I 80 GLN cc_start: 0.3112 (OUTLIER) cc_final: 0.2804 (pm20) REVERT: I 116 ARG cc_start: 0.3495 (mpt180) cc_final: 0.2068 (tpp-160) REVERT: I 147 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6344 (m-30) REVERT: K 212 GLU cc_start: 0.4556 (OUTLIER) cc_final: 0.3800 (mt-10) REVERT: K 214 MET cc_start: 0.4752 (mmm) cc_final: 0.4502 (mtt) REVERT: Q 163 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8508 (ptpp) outliers start: 116 outliers final: 77 residues processed: 221 average time/residue: 0.4350 time to fit residues: 155.8177 Evaluate side-chains 202 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 112 time to evaluate : 2.952 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 SER 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 389 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 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 103 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 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 85 ARG 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 45 TRP 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 210 MET Chi-restraints excluded: chain H residue 211 TRP 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 I residue 214 MET Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 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 196 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 227 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 118 optimal weight: 0.2980 chunk 255 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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** I 37 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.081296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.057950 restraints weight = 134097.814| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.13 r_work: 0.3223 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29572 Z= 0.162 Angle : 0.575 11.568 41470 Z= 0.305 Chirality : 0.038 0.193 4840 Planarity : 0.004 0.056 4076 Dihedral : 22.913 179.087 7921 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.24 % Allowed : 26.51 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2649 helix: 1.05 (0.13), residues: 1570 sheet: -1.35 (0.34), residues: 203 loop : -0.98 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 45 HIS 0.007 0.001 HIS F 77 PHE 0.011 0.001 PHE A 567 TYR 0.024 0.001 TYR H 73 ARG 0.004 0.000 ARG H 231 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1455) hydrogen bonds : angle 3.99088 ( 3996) metal coordination : bond 0.00702 ( 8) metal coordination : angle 2.22889 ( 9) covalent geometry : bond 0.00346 (29564) covalent geometry : angle 0.57447 (41461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 115 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 189 LYS cc_start: 0.8849 (tptp) cc_final: 0.8513 (tppt) REVERT: A 412 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7615 (t) REVERT: A 513 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8137 (mp10) REVERT: A 606 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8514 (mm) REVERT: E 196 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7107 (t80) REVERT: E 231 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8263 (mmp-170) REVERT: F 103 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8306 (tttp) REVERT: F 131 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: F 196 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: F 204 PHE cc_start: 0.8578 (m-10) cc_final: 0.8302 (m-80) REVERT: G 106 PHE cc_start: 0.8816 (m-80) cc_final: 0.8542 (m-80) REVERT: H 45 TRP cc_start: 0.3692 (OUTLIER) cc_final: 0.3062 (t60) REVERT: H 73 TYR cc_start: 0.6250 (t80) cc_final: 0.5919 (t80) REVERT: H 152 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: H 275 TYR cc_start: 0.1527 (m-80) cc_final: 0.1267 (m-80) REVERT: I 116 ARG cc_start: 0.3456 (mpt180) cc_final: 0.2133 (tpp-160) REVERT: I 147 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6412 (m-30) REVERT: K 85 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.4907 (ptm160) REVERT: K 212 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.3869 (mt-10) REVERT: Q 163 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8506 (ptpp) outliers start: 95 outliers final: 66 residues processed: 200 average time/residue: 0.4787 time to fit residues: 153.0982 Evaluate side-chains 191 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 111 time to evaluate : 3.474 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 120 GLU 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 276 SER 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 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 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 152 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 SER 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 196 PHE Chi-restraints excluded: chain F residue 206 ASN 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 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 45 TRP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 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 40 LEU 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 160 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 224 optimal weight: 30.0000 overall best weight: 5.3190 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.080314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.056795 restraints weight = 134185.366| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.38 r_work: 0.3175 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29572 Z= 0.269 Angle : 0.647 12.778 41470 Z= 0.341 Chirality : 0.042 0.199 4840 Planarity : 0.005 0.064 4076 Dihedral : 22.910 178.801 7921 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.37 % Allowed : 26.37 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2649 helix: 0.88 (0.13), residues: 1564 sheet: -1.77 (0.38), residues: 168 loop : -0.97 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 PHE 0.018 0.002 PHE A 567 TYR 0.027 0.002 TYR H 73 ARG 0.006 0.001 ARG G 243 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1455) hydrogen bonds : angle 4.11892 ( 3996) metal coordination : bond 0.00965 ( 8) metal coordination : angle 2.54793 ( 9) covalent geometry : bond 0.00576 (29564) covalent geometry : angle 0.64646 (41461) *********************** 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 207 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 109 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 412 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 513 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: A 606 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8519 (mm) REVERT: E 196 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7234 (t80) REVERT: E 231 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8278 (mmp-170) REVERT: F 103 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8417 (tttp) REVERT: F 131 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: F 196 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7966 (m-10) REVERT: F 204 PHE cc_start: 0.8558 (m-10) cc_final: 0.8285 (m-10) REVERT: G 106 PHE cc_start: 0.8836 (m-80) cc_final: 0.8525 (m-80) REVERT: H 45 TRP cc_start: 0.3727 (OUTLIER) cc_final: 0.3085 (t60) REVERT: H 95 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.5184 (ttp80) REVERT: H 275 TYR cc_start: 0.1497 (m-80) cc_final: 0.1223 (m-80) REVERT: I 61 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: I 116 ARG cc_start: 0.3417 (mpt180) cc_final: 0.2100 (tpp-160) REVERT: I 147 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: K 85 ARG cc_start: 0.5623 (OUTLIER) cc_final: 0.4931 (ptm160) REVERT: K 212 GLU cc_start: 0.4571 (OUTLIER) cc_final: 0.3898 (mt-10) REVERT: Q 163 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8529 (ptpp) outliers start: 98 outliers final: 74 residues processed: 197 average time/residue: 0.4046 time to fit residues: 128.9136 Evaluate side-chains 197 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 108 time to evaluate : 2.738 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 120 GLU 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 276 SER 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 598 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 152 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 SER 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 196 PHE Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN 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 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 45 TRP Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 232 ILE 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 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 13 LEU Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 40 LEU 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 70 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 271 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.080488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.056785 restraints weight = 133689.480| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.55 r_work: 0.3178 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29572 Z= 0.262 Angle : 0.651 12.001 41470 Z= 0.343 Chirality : 0.042 0.198 4840 Planarity : 0.005 0.060 4076 Dihedral : 22.914 179.246 7921 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.28 % Allowed : 26.51 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2649 helix: 0.82 (0.13), residues: 1560 sheet: -1.55 (0.37), residues: 198 loop : -1.04 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 PHE 0.016 0.002 PHE A 567 TYR 0.029 0.002 TYR H 73 ARG 0.006 0.001 ARG G 243 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 1455) hydrogen bonds : angle 4.15419 ( 3996) metal coordination : bond 0.01000 ( 8) metal coordination : angle 2.48665 ( 9) covalent geometry : bond 0.00561 (29564) covalent geometry : angle 0.65028 (41461) ********************** 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 206 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 110 time to evaluate : 3.532 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: 0.7913 (OUTLIER) cc_final: 0.7686 (t) REVERT: A 513 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: A 606 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8547 (mm) REVERT: E 196 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7243 (t80) REVERT: E 231 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8300 (mmp-170) REVERT: F 103 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8424 (tttp) REVERT: F 131 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: F 196 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: F 204 PHE cc_start: 0.8543 (m-10) cc_final: 0.8293 (m-10) REVERT: F 214 MET cc_start: 0.8172 (ptt) cc_final: 0.7861 (ppp) REVERT: G 106 PHE cc_start: 0.8811 (m-80) cc_final: 0.8519 (m-80) REVERT: H 73 TYR cc_start: 0.6276 (t80) cc_final: 0.5949 (t80) REVERT: H 275 TYR cc_start: 0.1362 (m-80) cc_final: 0.1120 (m-80) REVERT: I 61 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: I 116 ARG cc_start: 0.3330 (mpt180) cc_final: 0.2064 (tpp-160) REVERT: I 147 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: K 85 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.5019 (ptm160) REVERT: K 212 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.4018 (mt-10) REVERT: Q 163 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8503 (ptpp) REVERT: X 14 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8345 (pp20) outliers start: 96 outliers final: 77 residues processed: 197 average time/residue: 0.4944 time to fit residues: 159.0385 Evaluate side-chains 197 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 108 time to evaluate : 2.948 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 120 GLU 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 276 SER 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 598 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 152 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 SER 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 196 PHE Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN 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 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 142 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 211 TRP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 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 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 13 LEU Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 40 LEU 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 181 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4134 r_free = 0.4134 target = 0.081051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.056711 restraints weight = 134487.395| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.37 r_work: 0.3204 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2245 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= 0.174 Angle : 0.596 12.381 41470 Z= 0.314 Chirality : 0.039 0.194 4840 Planarity : 0.004 0.058 4076 Dihedral : 22.841 179.648 7919 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.24 % Allowed : 26.51 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2649 helix: 1.05 (0.13), residues: 1562 sheet: -1.50 (0.36), residues: 198 loop : -0.98 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 45 HIS 0.007 0.001 HIS F 77 PHE 0.012 0.001 PHE F 196 TYR 0.025 0.002 TYR H 73 ARG 0.013 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 1455) hydrogen bonds : angle 4.01397 ( 3996) metal coordination : bond 0.00695 ( 8) metal coordination : angle 2.33930 ( 9) covalent geometry : bond 0.00373 (29564) covalent geometry : angle 0.59522 (41461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23888.06 seconds wall clock time: 422 minutes 31.28 seconds (25351.28 seconds total)