Starting phenix.real_space_refine on Tue Feb 20 15:47:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2024/8bd5_15975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2024/8bd5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2024/8bd5_15975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2024/8bd5_15975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2024/8bd5_15975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bd5_15975/02_2024/8bd5_15975_updated.pdb" } 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 Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.45, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 14.13 Conformation dependent library (CDL) restraints added in 3.8 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... running ksdssp... Secondary structure from input PDB file: 126 helices and 12 sheets defined 55.2% alpha, 5.5% beta 118 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 13.04 Creating SS restraints... Processing helix chain 'A' and resid 14 through 25 removed outlier: 3.791A pdb=" N LEU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 43 through 50 removed outlier: 4.273A pdb=" N GLU A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 67 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 77 through 94 removed outlier: 3.704A pdb=" N SER A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.547A pdb=" N ASN A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.691A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 319 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 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 384 through 407 removed outlier: 3.583A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 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 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'A' and resid 485 through 506 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) Processing helix chain 'A' and resid 517 through 537 Processing helix chain 'A' and resid 551 through 566 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 571 through 576 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 619 through 634 Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 136 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 164 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 174 through 182 Processing helix chain 'E' and resid 184 through 189 removed outlier: 4.360A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 removed outlier: 3.691A pdb=" N GLU E 212 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET E 214 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 241 through 258 Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 151 through 164 Processing helix chain 'F' and resid 174 through 182 removed outlier: 3.852A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 203 through 213 removed outlier: 4.260A pdb=" N GLU F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 3.815A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.511A pdb=" N ARG G 74 " --> pdb=" O CYS G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 136 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 164 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 174 through 182 removed outlier: 3.551A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 202 through 213 Processing helix chain 'G' and resid 227 through 236 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 241 through 257 Processing helix chain 'G' and resid 265 through 275 Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 37 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 66 through 76 Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 181 Processing helix chain 'H' and resid 186 through 189 No H-bonds generated for 'chain 'H' and resid 186 through 189' Processing helix chain 'H' and resid 202 through 214 Processing helix chain 'H' and resid 227 through 237 Processing helix chain 'H' and resid 241 through 258 Processing helix chain 'H' and resid 265 through 273 Processing helix chain 'I' and resid 18 through 29 Processing helix chain 'I' and resid 37 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 66 through 76 Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 151 through 164 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 174 through 182 removed outlier: 3.755A pdb=" N ALA I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 189 Processing helix chain 'I' and resid 202 through 213 Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 241 through 258 Processing helix chain 'I' and resid 265 through 273 Processing helix chain 'J' and resid 18 through 29 Processing helix chain 'J' and resid 37 through 52 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 102 through 112 Processing helix chain 'J' and resid 122 through 136 Processing helix chain 'J' and resid 151 through 164 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 182 removed outlier: 3.654A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 189 Processing helix chain 'J' and resid 202 through 214 Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 273 Processing helix chain 'K' and resid 18 through 29 Processing helix chain 'K' and resid 37 through 52 removed outlier: 3.749A pdb=" N ALA K 52 " --> pdb=" O GLY K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 76 Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 136 Processing helix chain 'K' and resid 151 through 163 removed outlier: 4.204A pdb=" N ALA K 155 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP K 163 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 181 Processing helix chain 'K' and resid 185 through 189 Processing helix chain 'K' and resid 202 through 213 Processing helix chain 'K' and resid 227 through 237 Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 265 through 275 Processing helix chain 'Q' and resid 22 through 33 Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 47 through 55 removed outlier: 3.663A pdb=" N VAL Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU Q 54 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 74 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 78 through 84 removed outlier: 3.872A pdb=" N MET Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 106 Processing helix chain 'Q' and resid 112 through 115 Processing helix chain 'Q' and resid 143 through 145 No H-bonds generated for 'chain 'Q' and resid 143 through 145' Processing helix chain 'Q' and resid 160 through 163 Processing helix chain 'X' and resid 5 through 14 Processing helix chain 'X' and resid 25 through 45 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 50 through 73 removed outlier: 4.112A pdb=" N GLY X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 85 Processing sheet with id= A, first strand: chain 'A' and resid 314 through 316 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= B, first strand: chain 'A' and resid 291 through 295 Processing sheet with id= C, 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= D, first strand: chain 'A' and resid 542 through 546 removed outlier: 6.320A pdb=" N VAL A 607 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 545 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU A 609 " --> pdb=" O LEU A 545 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.905A pdb=" N MET E 140 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE E 94 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE E 142 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA E 167 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE E 143 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL E 169 " --> pdb=" O ILE E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.540A pdb=" N GLY F 172 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.868A pdb=" N MET G 140 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE G 94 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE G 142 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA G 167 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE G 143 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 169 " --> pdb=" O ILE G 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'H' and resid 193 through 195 removed outlier: 7.589A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU H 170 " --> pdb=" O CYS H 56 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY H 172 " --> pdb=" O VAL H 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.872A pdb=" N GLY I 172 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 92 " --> pdb=" O MET I 140 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 56 through 59 removed outlier: 6.240A pdb=" N ALA J 192 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL J 59 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU J 194 " --> pdb=" O VAL J 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'J' and resid 91 through 94 removed outlier: 7.137A pdb=" N MET J 140 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE J 94 " --> pdb=" O MET J 140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE J 142 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA J 167 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE J 143 " --> pdb=" O ALA J 167 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL J 169 " --> pdb=" O ILE J 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.087A pdb=" N MET K 140 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE K 94 " --> pdb=" O MET K 140 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE K 142 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA K 167 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE K 143 " --> pdb=" O ALA K 167 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL K 169 " --> pdb=" O ILE K 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 988 hydrogen bonds defined for protein. 2874 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: 11.36 Time building geometry restraints manager: 14.90 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: 98.42 - 106.71: 2460 106.71 - 115.00: 18503 115.00 - 123.29: 18198 123.29 - 131.58: 2159 131.58 - 139.88: 141 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: 297 2.57 - 3.15: 23076 3.15 - 3.73: 52229 3.73 - 4.32: 67994 4.32 - 4.90: 102759 Nonbonded interactions: 246355 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 246350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 24.270 Check model and map are aligned: 0.570 Set scattering table: 0.250 Process input model: 90.240 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.170 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.420 ------------------------------------------------------------------------------- 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 0.050 29564 Z= 0.239 Angle : 0.623 9.062 41461 Z= 0.354 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 *********************** 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 fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 3.117 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: 0.4400 time to fit residues: 80.2013 Evaluate side-chains 107 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 2.859 ------------------------------------------------------------------------------- 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: 0.9980 chunk 225 optimal weight: 20.0000 chunk 125 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 173 optimal weight: 30.0000 chunk 270 optimal weight: 10.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29564 Z= 0.227 Angle : 0.555 7.721 41461 Z= 0.296 Chirality : 0.038 0.182 4840 Planarity : 0.004 0.069 4076 Dihedral : 23.282 179.810 7933 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.57 % Allowed : 25.17 % Favored : 71.26 % 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: 0.28 (0.16), residues: 2649 helix: 1.15 (0.14), residues: 1527 sheet: -1.59 (0.43), residues: 141 loop : -1.02 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 45 HIS 0.006 0.001 HIS J 77 PHE 0.014 0.001 PHE H 106 TYR 0.020 0.001 TYR H 73 ARG 0.004 0.000 ARG H 148 *********************** 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 183 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 103 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7523 (t0) REVERT: F 147 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: G 75 TYR cc_start: 0.9055 (m-80) cc_final: 0.8592 (m-80) REVERT: G 95 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7327 (ptm-80) REVERT: G 98 GLN cc_start: 0.8245 (tp40) cc_final: 0.7811 (tp40) REVERT: G 106 PHE cc_start: 0.8840 (m-80) cc_final: 0.8510 (m-80) REVERT: H 190 PHE cc_start: 0.5832 (m-10) cc_final: 0.5618 (m-10) REVERT: H 275 TYR cc_start: 0.1152 (m-80) cc_final: 0.0924 (m-80) REVERT: I 80 GLN cc_start: 0.3532 (OUTLIER) cc_final: 0.3110 (pm20) REVERT: K 214 MET cc_start: 0.4530 (mmm) cc_final: 0.3226 (ptm) outliers start: 80 outliers final: 39 residues processed: 170 average time/residue: 0.3862 time to fit residues: 107.4407 Evaluate side-chains 142 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR 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 E residue 58 VAL Chi-restraints excluded: chain E residue 125 PHE 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 67 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 143 ILE 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 J residue 45 TRP Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 80 GLN 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 K residue 276 LYS Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 42 THR 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 150 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 271 optimal weight: 30.0000 chunk 292 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 217 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 29564 Z= 0.448 Angle : 0.682 8.075 41461 Z= 0.361 Chirality : 0.044 0.218 4840 Planarity : 0.005 0.065 4076 Dihedral : 23.278 177.554 7922 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.22 % Allowed : 25.08 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.16), residues: 2649 helix: 0.78 (0.13), residues: 1527 sheet: -1.13 (0.33), residues: 245 loop : -1.32 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 45 HIS 0.009 0.002 HIS A 586 PHE 0.018 0.002 PHE A 567 TYR 0.022 0.002 TYR H 73 ARG 0.013 0.001 ARG E 116 *********************** 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 222 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 105 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7858 (t70) REVERT: A 322 LEU cc_start: 0.8937 (tp) cc_final: 0.8652 (mt) REVERT: E 196 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7180 (t80) REVERT: F 128 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7446 (mtp180) REVERT: F 131 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: G 75 TYR cc_start: 0.9070 (m-80) cc_final: 0.8758 (m-80) REVERT: G 95 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7460 (ptm-80) REVERT: K 214 MET cc_start: 0.4433 (mmm) cc_final: 0.4134 (mtt) outliers start: 117 outliers final: 68 residues processed: 206 average time/residue: 0.4294 time to fit residues: 144.0199 Evaluate side-chains 176 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 103 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 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 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 128 ARG 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 42 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 80 GLN 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 K residue 276 LYS Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 42 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 0.6980 chunk 203 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 288 optimal weight: 0.4980 chunk 142 optimal weight: 40.0000 chunk 257 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** E 43 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 GLN X 20 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29564 Z= 0.156 Angle : 0.529 9.184 41461 Z= 0.282 Chirality : 0.037 0.179 4840 Planarity : 0.004 0.056 4076 Dihedral : 23.131 179.070 7922 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.48 % Allowed : 26.77 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2649 helix: 1.20 (0.14), residues: 1531 sheet: -0.90 (0.34), residues: 243 loop : -1.13 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 45 HIS 0.007 0.001 HIS G 97 PHE 0.014 0.001 PHE J 204 TYR 0.030 0.001 TYR K 75 ARG 0.003 0.000 ARG I 128 *********************** 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 196 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 118 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 196 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6851 (t80) REVERT: F 147 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: F 204 PHE cc_start: 0.8230 (m-80) cc_final: 0.7935 (m-80) REVERT: F 276 LYS cc_start: 0.6914 (mppt) cc_final: 0.6676 (mptt) REVERT: G 75 TYR cc_start: 0.9048 (m-80) cc_final: 0.8723 (m-80) REVERT: G 106 PHE cc_start: 0.8821 (m-80) cc_final: 0.8539 (m-80) REVERT: I 80 GLN cc_start: 0.3596 (OUTLIER) cc_final: 0.3155 (pm20) REVERT: I 116 ARG cc_start: 0.3401 (mpt180) cc_final: 0.1742 (tpp-160) REVERT: K 80 GLN cc_start: 0.2501 (OUTLIER) cc_final: 0.2204 (pp30) REVERT: K 214 MET cc_start: 0.4387 (mmm) cc_final: 0.4088 (mtt) outliers start: 78 outliers final: 35 residues processed: 183 average time/residue: 0.3995 time to fit residues: 116.7225 Evaluate side-chains 146 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 80 GLN 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 13 LEU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 20 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 4 optimal weight: 0.1980 chunk 214 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 245 optimal weight: 40.0000 chunk 199 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 147 optimal weight: 30.0000 chunk 258 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- 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** E 43 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29564 Z= 0.360 Angle : 0.623 13.327 41461 Z= 0.329 Chirality : 0.041 0.190 4840 Planarity : 0.005 0.063 4076 Dihedral : 23.104 178.111 7922 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.82 % Allowed : 25.97 % 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: 0.07 (0.16), residues: 2649 helix: 0.97 (0.13), residues: 1528 sheet: -1.00 (0.33), residues: 245 loop : -1.21 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 45 HIS 0.008 0.001 HIS A 586 PHE 0.015 0.002 PHE A 401 TYR 0.022 0.002 TYR H 73 ARG 0.005 0.001 ARG A 616 *********************** 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 218 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 110 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: E 196 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7068 (t80) REVERT: E 231 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8101 (mmt180) REVERT: F 128 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7433 (mtp180) REVERT: F 147 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: F 204 PHE cc_start: 0.8230 (m-10) cc_final: 0.7988 (m-80) REVERT: F 276 LYS cc_start: 0.7063 (mppt) cc_final: 0.6750 (mptt) REVERT: G 75 TYR cc_start: 0.9091 (m-80) cc_final: 0.8830 (m-80) REVERT: G 95 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7467 (ptm-80) REVERT: I 80 GLN cc_start: 0.3553 (OUTLIER) cc_final: 0.3123 (pm20) REVERT: I 116 ARG cc_start: 0.3457 (mpt180) cc_final: 0.1820 (tpp-160) REVERT: K 212 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.3822 (mt-10) REVERT: K 214 MET cc_start: 0.4413 (mmm) cc_final: 0.4116 (mtt) outliers start: 108 outliers final: 72 residues processed: 205 average time/residue: 0.4023 time to fit residues: 133.0399 Evaluate side-chains 186 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 106 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 104 ASP 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 G residue 253 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 275 TYR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 24 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 288 optimal weight: 0.9990 chunk 239 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 151 optimal weight: 0.0980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29564 Z= 0.137 Angle : 0.520 13.323 41461 Z= 0.274 Chirality : 0.036 0.177 4840 Planarity : 0.004 0.049 4076 Dihedral : 22.992 177.918 7922 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.30 % Allowed : 27.84 % Favored : 68.85 % 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: 0.47 (0.17), residues: 2649 helix: 1.31 (0.14), residues: 1533 sheet: -0.89 (0.33), residues: 243 loop : -1.05 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 45 HIS 0.005 0.001 HIS A 304 PHE 0.014 0.001 PHE G 106 TYR 0.016 0.001 TYR H 73 ARG 0.004 0.000 ARG X 17 *********************** 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 191 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 117 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: A 606 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8424 (mm) REVERT: E 196 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6812 (t80) REVERT: E 231 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8077 (mmt180) REVERT: F 147 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7059 (m-30) REVERT: F 204 PHE cc_start: 0.8264 (m-10) cc_final: 0.7988 (m-10) REVERT: F 276 LYS cc_start: 0.6888 (mppt) cc_final: 0.6610 (mptt) REVERT: G 75 TYR cc_start: 0.9074 (m-80) cc_final: 0.8786 (m-80) REVERT: G 106 PHE cc_start: 0.8842 (m-80) cc_final: 0.8593 (m-80) REVERT: I 80 GLN cc_start: 0.3553 (OUTLIER) cc_final: 0.3129 (pm20) REVERT: I 116 ARG cc_start: 0.3329 (mpt180) cc_final: 0.1731 (tpp-160) REVERT: K 80 GLN cc_start: 0.2406 (OUTLIER) cc_final: 0.2068 (pm20) REVERT: K 214 MET cc_start: 0.4411 (mmm) cc_final: 0.4126 (mtt) REVERT: Q 163 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8356 (ptpp) outliers start: 74 outliers final: 40 residues processed: 183 average time/residue: 0.4226 time to fit residues: 123.7681 Evaluate side-chains 157 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 110 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 140 MET 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 143 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 80 GLN 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 13 LEU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 164 optimal weight: 0.0020 chunk 210 optimal weight: 9.9990 chunk 163 optimal weight: 30.0000 chunk 242 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN E 43 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29564 Z= 0.331 Angle : 0.602 12.819 41461 Z= 0.318 Chirality : 0.040 0.187 4840 Planarity : 0.004 0.063 4076 Dihedral : 22.969 178.485 7922 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.15 % Allowed : 27.26 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.13), residues: 1541 sheet: -0.89 (0.34), residues: 233 loop : -1.10 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 45 HIS 0.008 0.001 HIS A 586 PHE 0.014 0.002 PHE A 401 TYR 0.022 0.002 TYR H 73 ARG 0.008 0.001 ARG E 189 *********************** 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 201 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 108 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: A 606 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8426 (mm) REVERT: E 196 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7035 (t80) REVERT: E 231 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8118 (mmt180) REVERT: F 147 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: F 204 PHE cc_start: 0.8293 (m-10) cc_final: 0.8016 (m-80) REVERT: F 276 LYS cc_start: 0.7004 (mppt) cc_final: 0.6675 (mptt) REVERT: G 75 TYR cc_start: 0.9087 (m-80) cc_final: 0.8854 (m-80) REVERT: G 85 ARG cc_start: 0.5097 (OUTLIER) cc_final: 0.4853 (ttp-170) REVERT: G 95 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7483 (ptm-80) REVERT: G 106 PHE cc_start: 0.8835 (m-80) cc_final: 0.8455 (m-80) REVERT: I 80 GLN cc_start: 0.3526 (OUTLIER) cc_final: 0.3095 (pm20) REVERT: I 116 ARG cc_start: 0.3436 (mpt180) cc_final: 0.1862 (tpp-160) REVERT: K 80 GLN cc_start: 0.2369 (OUTLIER) cc_final: 0.1978 (pm20) REVERT: K 212 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.3695 (mt-10) REVERT: K 214 MET cc_start: 0.4590 (mmm) cc_final: 0.4310 (mtt) outliers start: 93 outliers final: 62 residues processed: 187 average time/residue: 0.3926 time to fit residues: 118.3869 Evaluate side-chains 179 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 107 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 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 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 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 E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 67 THR 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 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 140 MET 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 121 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 179 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 80 GLN 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 K residue 276 LYS Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 94 HIS Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 24 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 0.0010 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 142 optimal weight: 40.0000 chunk 26 optimal weight: 4.9990 chunk 225 optimal weight: 30.0000 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29564 Z= 0.192 Angle : 0.535 12.687 41461 Z= 0.284 Chirality : 0.037 0.179 4840 Planarity : 0.004 0.051 4076 Dihedral : 22.938 179.054 7922 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.75 % Allowed : 27.44 % Favored : 68.81 % 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: 0.33 (0.17), residues: 2649 helix: 1.14 (0.13), residues: 1552 sheet: -0.88 (0.34), residues: 233 loop : -1.09 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 45 HIS 0.018 0.001 HIS K 43 PHE 0.010 0.001 PHE J 204 TYR 0.019 0.001 TYR H 73 ARG 0.012 0.000 ARG E 189 *********************** 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 195 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 111 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: A 606 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8429 (mm) REVERT: E 196 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6929 (t80) REVERT: E 231 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8100 (mmt180) REVERT: F 147 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: F 204 PHE cc_start: 0.8278 (m-10) cc_final: 0.8009 (m-80) REVERT: F 276 LYS cc_start: 0.6968 (mppt) cc_final: 0.6667 (mptt) REVERT: G 75 TYR cc_start: 0.9082 (m-80) cc_final: 0.8813 (m-80) REVERT: G 106 PHE cc_start: 0.8822 (m-80) cc_final: 0.8455 (m-80) REVERT: H 275 TYR cc_start: 0.1359 (m-80) cc_final: 0.1111 (m-80) REVERT: I 80 GLN cc_start: 0.3487 (OUTLIER) cc_final: 0.3084 (pm20) REVERT: I 116 ARG cc_start: 0.3342 (mpt180) cc_final: 0.1840 (tpp-160) REVERT: K 80 GLN cc_start: 0.2304 (OUTLIER) cc_final: 0.1944 (pm20) REVERT: K 214 MET cc_start: 0.4613 (mmm) cc_final: 0.4335 (mtt) REVERT: Q 54 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7502 (mp0) outliers start: 84 outliers final: 59 residues processed: 185 average time/residue: 0.4059 time to fit residues: 119.8296 Evaluate side-chains 176 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 109 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER 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 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 426 LEU 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 598 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 104 ASP 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 196 PHE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 121 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 179 VAL Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 80 GLN 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 275 TYR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 24 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 0.9980 chunk 275 optimal weight: 0.7980 chunk 251 optimal weight: 30.0000 chunk 267 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 210 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 266 optimal weight: 0.5980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29564 Z= 0.163 Angle : 0.522 12.497 41461 Z= 0.276 Chirality : 0.036 0.173 4840 Planarity : 0.004 0.055 4076 Dihedral : 22.789 179.582 7922 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.99 % Allowed : 28.25 % Favored : 68.76 % 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: 0.49 (0.17), residues: 2649 helix: 1.30 (0.14), residues: 1543 sheet: -0.77 (0.34), residues: 231 loop : -1.08 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 45 HIS 0.004 0.001 HIS H 43 PHE 0.010 0.001 PHE J 204 TYR 0.015 0.001 TYR K 112 ARG 0.008 0.000 ARG E 189 *********************** 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 180 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 113 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: A 606 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8388 (mm) REVERT: E 196 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6887 (t80) REVERT: E 231 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8078 (mmt180) REVERT: F 147 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: F 204 PHE cc_start: 0.8254 (m-10) cc_final: 0.7968 (m-80) REVERT: F 276 LYS cc_start: 0.6946 (mppt) cc_final: 0.6642 (mptt) REVERT: G 106 PHE cc_start: 0.8810 (m-80) cc_final: 0.8489 (m-80) REVERT: H 275 TYR cc_start: 0.1334 (m-80) cc_final: 0.1091 (m-80) REVERT: I 80 GLN cc_start: 0.3533 (OUTLIER) cc_final: 0.3122 (pm20) REVERT: I 116 ARG cc_start: 0.3280 (mpt180) cc_final: 0.1827 (tpp-160) REVERT: K 80 GLN cc_start: 0.2228 (OUTLIER) cc_final: 0.1863 (pm20) REVERT: K 214 MET cc_start: 0.4634 (mmm) cc_final: 0.4353 (mtt) REVERT: Q 54 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: Q 163 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8346 (ptpp) outliers start: 67 outliers final: 56 residues processed: 171 average time/residue: 0.3930 time to fit residues: 108.5915 Evaluate side-chains 172 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 108 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 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 E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 67 THR 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 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 140 MET 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 121 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 179 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 80 GLN 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 276 LYS Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 196 optimal weight: 40.0000 chunk 296 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 0.0870 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 213 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29564 Z= 0.244 Angle : 0.555 12.157 41461 Z= 0.293 Chirality : 0.038 0.175 4840 Planarity : 0.004 0.055 4076 Dihedral : 22.782 179.889 7922 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.35 % Allowed : 27.98 % Favored : 68.67 % 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: 0.39 (0.17), residues: 2649 helix: 1.19 (0.13), residues: 1549 sheet: -0.83 (0.34), residues: 233 loop : -1.07 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 45 HIS 0.006 0.001 HIS A 586 PHE 0.011 0.001 PHE A 567 TYR 0.016 0.001 TYR A 91 ARG 0.007 0.000 ARG E 189 ********************** 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 186 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 111 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: A 606 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8428 (mm) REVERT: E 196 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6972 (t80) REVERT: E 231 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8099 (mmt180) REVERT: F 147 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: F 204 PHE cc_start: 0.8279 (m-10) cc_final: 0.7970 (m-80) REVERT: F 276 LYS cc_start: 0.7076 (mppt) cc_final: 0.6769 (mptt) REVERT: G 85 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4806 (ttp-170) REVERT: G 95 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7477 (ptm-80) REVERT: G 106 PHE cc_start: 0.8812 (m-80) cc_final: 0.8432 (m-80) REVERT: H 275 TYR cc_start: 0.1314 (m-80) cc_final: 0.1072 (m-80) REVERT: I 116 ARG cc_start: 0.3331 (mpt180) cc_final: 0.1877 (tpp-160) REVERT: K 212 GLU cc_start: 0.4740 (OUTLIER) cc_final: 0.3842 (mt-10) REVERT: K 214 MET cc_start: 0.4632 (mmm) cc_final: 0.4342 (mtt) REVERT: Q 54 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7515 (mp0) outliers start: 75 outliers final: 60 residues processed: 176 average time/residue: 0.4189 time to fit residues: 117.1570 Evaluate side-chains 178 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 109 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 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 E residue 58 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 67 THR 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 147 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 121 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 179 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 230 LEU 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 276 LYS Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain X residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 30.0000 chunk 251 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 185 GLN ** 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 = 0.4138 r_free = 0.4138 target = 0.081181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057618 restraints weight = 133624.709| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.23 r_work: 0.3213 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29564 Z= 0.277 Angle : 0.585 11.722 41461 Z= 0.308 Chirality : 0.039 0.174 4840 Planarity : 0.004 0.057 4076 Dihedral : 22.824 179.741 7919 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.17 % Allowed : 28.16 % Favored : 68.67 % 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: 0.26 (0.17), residues: 2649 helix: 1.09 (0.13), residues: 1525 sheet: -1.05 (0.33), residues: 247 loop : -1.00 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 45 HIS 0.006 0.001 HIS A 586 PHE 0.012 0.002 PHE A 401 TYR 0.024 0.002 TYR H 73 ARG 0.007 0.000 ARG E 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5490.92 seconds wall clock time: 101 minutes 52.94 seconds (6112.94 seconds total)