Starting phenix.real_space_refine on Sat Jul 4 02:49:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oci_12808/07_2026/7oci_12808.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 11237 2.51 5 N 2663 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17077 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3503 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 869 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 5130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5130 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 615} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 376} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1873 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 15, 'TRANS': 242} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'AJP': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'AJP': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 19 Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {' MG': 1, 'PEE': 1, 'V8K': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 3.25, per 1000 atoms: 0.19 Number of scatterers: 17077 At special positions: 0 Unit cell: (152.04, 110.88, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 7 15.00 Mg 1 11.99 O 3114 8.00 N 2663 7.00 C 11237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1302 " - " ASN A 400 " " NAG G 501 " - " ASN G 332 " " NAG G 502 " - " ASN G 60 " " NAG J 1 " - " ASN F 539 " " NAG K 1 " - " ASN A 336 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 545.9 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 21 sheets defined 45.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.670A pdb=" N SER A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 447 through 470 removed outlier: 3.695A pdb=" N LEU A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.791A pdb=" N ARG B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 68 removed outlier: 4.003A pdb=" N ASP B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 54 " --> pdb=" O PHE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.702A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 130 removed outlier: 3.556A pdb=" N ALA B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 129 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 232 removed outlier: 3.774A pdb=" N ILE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 3.553A pdb=" N THR C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 264 through 288 removed outlier: 3.548A pdb=" N ILE C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 295 through 325 removed outlier: 4.224A pdb=" N ILE C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 33 removed outlier: 3.673A pdb=" N LEU D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 23 " --> pdb=" O MET D 19 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.851A pdb=" N HIS E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 49 removed outlier: 3.805A pdb=" N PHE E 28 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL E 35 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 43 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 83 removed outlier: 4.481A pdb=" N LEU E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE E 66 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 31 removed outlier: 3.663A pdb=" N PHE F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.666A pdb=" N ILE F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS F 38 " --> pdb=" O PHE F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 33 through 38' Processing helix chain 'F' and resid 47 through 61 removed outlier: 3.877A pdb=" N ASN F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 89 through 104 Processing helix chain 'F' and resid 110 through 138 removed outlier: 4.816A pdb=" N ALA F 119 " --> pdb=" O CYS F 115 " (cutoff:3.500A) Proline residue: F 120 - end of helix removed outlier: 3.987A pdb=" N GLY F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE F 137 " --> pdb=" O PHE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 removed outlier: 4.317A pdb=" N LEU F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 167 through 189 removed outlier: 5.192A pdb=" N THR F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU F 174 " --> pdb=" O ILE F 170 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 179 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 208 removed outlier: 3.642A pdb=" N CYS F 196 " --> pdb=" O MET F 192 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA F 197 " --> pdb=" O HIS F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 228 removed outlier: 4.297A pdb=" N ILE F 214 " --> pdb=" O GLY F 210 " (cutoff:3.500A) Proline residue: F 219 - end of helix Processing helix chain 'F' and resid 232 through 251 removed outlier: 4.062A pdb=" N TYR F 236 " --> pdb=" O SER F 232 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 263 through 288 removed outlier: 3.767A pdb=" N MET F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA F 268 " --> pdb=" O ASN F 264 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 362 removed outlier: 3.640A pdb=" N PHE F 360 " --> pdb=" O TRP F 356 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 362 " --> pdb=" O ALA F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 380 removed outlier: 4.183A pdb=" N ASP F 380 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.509A pdb=" N VAL F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 430 removed outlier: 3.715A pdb=" N LEU F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Proline residue: F 411 - end of helix removed outlier: 3.634A pdb=" N LYS F 423 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 473 removed outlier: 3.990A pdb=" N ALA F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER F 454 " --> pdb=" O ILE F 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP F 468 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR F 470 " --> pdb=" O SER F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 507 removed outlier: 3.571A pdb=" N ALA F 499 " --> pdb=" O ASP F 495 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 540 through 550 removed outlier: 3.807A pdb=" N VAL F 546 " --> pdb=" O HIS F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 561 removed outlier: 3.997A pdb=" N GLU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 596 removed outlier: 3.542A pdb=" N MET F 590 " --> pdb=" O LYS F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 4.181A pdb=" N PHE F 607 " --> pdb=" O LYS F 603 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR F 608 " --> pdb=" O GLU F 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 603 through 608' Processing helix chain 'F' and resid 627 through 634 removed outlier: 3.605A pdb=" N LYS F 631 " --> pdb=" O SER F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 641 removed outlier: 4.314A pdb=" N PHE F 641 " --> pdb=" O PHE F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 691 through 701 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 40 through 49 Processing helix chain 'G' and resid 86 through 94 removed outlier: 4.540A pdb=" N LEU G 90 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 removed outlier: 3.785A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 130 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 211 through 215 removed outlier: 4.028A pdb=" N GLN G 214 " --> pdb=" O SER G 211 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY G 215 " --> pdb=" O GLY G 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 215' Processing helix chain 'G' and resid 246 through 258 removed outlier: 3.683A pdb=" N LYS G 255 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 383 removed outlier: 3.764A pdb=" N TYR G 383 " --> pdb=" O ASN G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 414 removed outlier: 3.671A pdb=" N SER G 397 " --> pdb=" O TRP G 393 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA G 398 " --> pdb=" O VAL G 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE G 399 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL G 414 " --> pdb=" O VAL G 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 129 removed outlier: 3.507A pdb=" N LEU H 123 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG H 128 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 216 removed outlier: 3.802A pdb=" N ALA H 196 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 252 removed outlier: 3.623A pdb=" N GLU H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 282 removed outlier: 3.554A pdb=" N LEU H 267 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix removed outlier: 3.782A pdb=" N LEU H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 21 removed outlier: 3.951A pdb=" N UNK I 10 " --> pdb=" O UNK I 6 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N UNK I 21 " --> pdb=" O UNK I 17 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 84 removed outlier: 3.655A pdb=" N PHE A 80 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A 56 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN A 33 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N SER A 174 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 36 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR A 176 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 38 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 178 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 40 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 175 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 310 removed outlier: 5.515A pdb=" N ASP A 301 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR A 342 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 237 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 235 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 258 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL A 233 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLU A 378 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 236 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N SER A 380 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 238 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 382 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 240 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.505A pdb=" N HIS A 320 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 351 removed outlier: 6.898A pdb=" N LEU A 436 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 392 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS A 438 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AA8, first strand: chain 'C' and resid 246 through 247 removed outlier: 4.788A pdb=" N ALA C 246 " --> pdb=" O MET C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'F' and resid 530 through 531 removed outlier: 6.553A pdb=" N LYS F 512 " --> pdb=" O TYR F 568 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU F 570 " --> pdb=" O LYS F 512 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA F 514 " --> pdb=" O LEU F 570 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ILE F 572 " --> pdb=" O ALA F 514 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN F 681 " --> pdb=" O GLU F 668 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU F 668 " --> pdb=" O GLN F 681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 646 through 647 Processing sheet with id=AB3, first strand: chain 'G' and resid 55 through 57 removed outlier: 6.200A pdb=" N VAL G 28 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE G 79 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET G 112 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL G 81 " --> pdb=" O MET G 112 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE G 109 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE G 232 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS G 111 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'G' and resid 139 through 141 removed outlier: 3.586A pdb=" N VAL G 139 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AB7, first strand: chain 'G' and resid 263 through 273 removed outlier: 3.920A pdb=" N VAL G 263 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY G 295 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA G 269 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER G 293 " --> pdb=" O ALA G 269 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS G 271 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE G 291 " --> pdb=" O HIS G 271 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS G 273 " --> pdb=" O LYS G 289 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS G 289 " --> pdb=" O HIS G 273 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR G 340 " --> pdb=" O PRO G 329 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 304 through 306 removed outlier: 3.526A pdb=" N PHE G 344 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 321 through 326 removed outlier: 6.599A pdb=" N LEU G 316 " --> pdb=" O TYR G 322 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG G 324 " --> pdb=" O PHE G 314 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE G 314 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 358 through 359 Processing sheet with id=AC2, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.651A pdb=" N VAL H 59 " --> pdb=" O PHE H 70 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN H 67 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY H 33 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 26 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N TYR H 109 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE H 28 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR H 111 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER H 30 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE H 113 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA H 32 " --> pdb=" O ILE H 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 92 through 96 removed outlier: 6.624A pdb=" N LEU H 137 " --> pdb=" O GLU H 153 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU H 153 " --> pdb=" O LEU H 137 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2618 1.32 - 1.45: 5153 1.45 - 1.58: 9648 1.58 - 1.72: 14 1.72 - 1.85: 93 Bond restraints: 17526 Sorted by residual: bond pdb=" C45 V8K F 903 " pdb=" C46 V8K F 903 " ideal model delta sigma weight residual 1.345 1.542 -0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" O56 V8K F 903 " pdb=" P57 V8K F 903 " ideal model delta sigma weight residual 1.716 1.851 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C30 PEE D 101 " pdb=" O3 PEE D 101 " ideal model delta sigma weight residual 1.327 1.436 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C30 PEE C1801 " pdb=" O3 PEE C1801 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C30 PEE B 201 " pdb=" O3 PEE B 201 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 17521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 23502 3.38 - 6.76: 249 6.76 - 10.14: 39 10.14 - 13.52: 5 13.52 - 16.90: 6 Bond angle restraints: 23801 Sorted by residual: angle pdb=" O3P PEE D 101 " pdb=" P PEE D 101 " pdb=" O4P PEE D 101 " ideal model delta sigma weight residual 92.91 109.81 -16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" O3P PEE H1101 " pdb=" P PEE H1101 " pdb=" O4P PEE H1101 " ideal model delta sigma weight residual 92.91 109.72 -16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O3P PEE B 201 " pdb=" P PEE B 201 " pdb=" O4P PEE B 201 " ideal model delta sigma weight residual 92.91 109.52 -16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O3P PEE F 902 " pdb=" P PEE F 902 " pdb=" O4P PEE F 902 " ideal model delta sigma weight residual 92.91 109.51 -16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O3P PEE A1301 " pdb=" P PEE A1301 " pdb=" O4P PEE A1301 " ideal model delta sigma weight residual 92.91 109.38 -16.47 3.00e+00 1.11e-01 3.01e+01 ... (remaining 23796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 9834 33.67 - 67.34: 215 67.34 - 101.01: 18 101.01 - 134.69: 11 134.69 - 168.36: 1 Dihedral angle restraints: 10079 sinusoidal: 3933 harmonic: 6146 Sorted by residual: dihedral pdb=" CA TRP F 75 " pdb=" C TRP F 75 " pdb=" N TYR F 76 " pdb=" CA TYR F 76 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C32 PEE C1801 " pdb=" C30 PEE C1801 " pdb=" C31 PEE C1801 " pdb=" O3 PEE C1801 " ideal model delta sinusoidal sigma weight residual 161.16 -30.48 -168.36 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C36 PEE A1301 " pdb=" C37 PEE A1301 " pdb=" C38 PEE A1301 " pdb=" C39 PEE A1301 " ideal model delta sinusoidal sigma weight residual 180.60 49.08 131.52 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 10076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.191: 2677 1.191 - 2.382: 0 2.382 - 3.573: 0 3.573 - 4.764: 9 4.764 - 5.954: 28 Chirality restraints: 2714 Sorted by residual: chirality pdb=" C12 AJP B 202 " pdb=" C07 AJP B 202 " pdb=" C11 AJP B 202 " pdb=" C13 AJP B 202 " both_signs ideal model delta sigma weight residual False 3.01 -2.95 5.95 2.00e-01 2.50e+01 8.86e+02 chirality pdb=" C12 AJP D 102 " pdb=" C07 AJP D 102 " pdb=" C11 AJP D 102 " pdb=" C13 AJP D 102 " both_signs ideal model delta sigma weight residual False 3.01 -2.87 5.88 2.00e-01 2.50e+01 8.64e+02 chirality pdb=" C20 AJP B 202 " pdb=" C15 AJP B 202 " pdb=" C19 AJP B 202 " pdb=" C21 AJP B 202 " both_signs ideal model delta sigma weight residual False 2.96 -2.90 5.86 2.00e-01 2.50e+01 8.58e+02 ... (remaining 2711 not shown) Planarity restraints: 2926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C44 V8K F 903 " -0.066 2.00e-02 2.50e+03 6.64e-02 4.41e+01 pdb=" C45 V8K F 903 " 0.063 2.00e-02 2.50e+03 pdb=" C46 V8K F 903 " 0.070 2.00e-02 2.50e+03 pdb=" C47 V8K F 903 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 145 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO H 146 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 426 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ASP F 426 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP F 426 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE F 427 " 0.017 2.00e-02 2.50e+03 ... (remaining 2923 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 430 2.70 - 3.25: 16913 3.25 - 3.80: 25137 3.80 - 4.35: 32522 4.35 - 4.90: 56937 Nonbonded interactions: 131939 Sorted by model distance: nonbonded pdb=" OD2 ASP D 29 " pdb=" OG SER F 141 " model vdw 2.155 3.040 nonbonded pdb=" OE2 GLU A 378 " pdb=" OG1 THR A 420 " model vdw 2.186 3.040 nonbonded pdb=" O LYS H 77 " pdb=" OG SER H 141 " model vdw 2.191 3.040 nonbonded pdb=" O GLY F 580 " pdb=" ND2 ASN F 585 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR H 136 " pdb=" O ARG H 152 " model vdw 2.263 3.040 ... (remaining 131934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.006 0.197 17538 Z= 0.294 Angle : 0.863 16.900 23837 Z= 0.368 Chirality : 0.592 5.954 2714 Planarity : 0.006 0.084 2921 Dihedral : 14.939 168.356 6111 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.17), residues: 2047 helix: -0.90 (0.17), residues: 829 sheet: -1.95 (0.24), residues: 400 loop : -2.36 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 619 TYR 0.030 0.001 TYR F 391 PHE 0.018 0.001 PHE F 223 TRP 0.020 0.001 TRP F 598 HIS 0.005 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.29 (17526) covalent geometry : angle 0.85999 / 0.37 (23801) hydrogen bonds : bond 0.14036 / 8.83 ( 744) hydrogen bonds : angle 6.33414 / 4.44 ( 2145) link_ALPHA1-2 : bond 0.00086 / 0.04 ( 2) link_ALPHA1-2 : angle 2.03613 / 1.23 ( 6) link_ALPHA1-3 : bond 0.00363 / 0.19 ( 1) link_ALPHA1-3 : angle 2.14286 / 1.15 ( 3) link_ALPHA1-6 : bond 0.00541 / 0.28 ( 1) link_ALPHA1-6 : angle 1.51856 / 0.86 ( 3) link_BETA1-4 : bond 0.00441 / 0.21 ( 3) link_BETA1-4 : angle 2.37862 / 1.38 ( 9) link_NAG-ASN : bond 0.00305 / 0.16 ( 5) link_NAG-ASN : angle 1.96035 / 1.04 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.8375 (ptp) cc_final: 0.8085 (ptp) REVERT: F 528 ASP cc_start: 0.8505 (t0) cc_final: 0.8199 (t0) REVERT: F 548 LYS cc_start: 0.8832 (tttt) cc_final: 0.8592 (tttp) REVERT: G 57 LEU cc_start: 0.8663 (tp) cc_final: 0.8386 (tt) REVERT: G 106 GLU cc_start: 0.8310 (mp0) cc_final: 0.7909 (mt-10) REVERT: G 171 ASP cc_start: 0.7989 (m-30) cc_final: 0.7421 (p0) REVERT: G 236 ASP cc_start: 0.8354 (t0) cc_final: 0.8139 (t0) REVERT: G 381 ASP cc_start: 0.7492 (t70) cc_final: 0.7048 (t0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1146 time to fit residues: 53.1783 Evaluate side-chains 244 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN B 97 GLN G 156 ASN G 242 ASN G 391 ASN H 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.108327 restraints weight = 20445.115| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.37 r_work: 0.2916 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17538 Z= 0.157 Angle : 1.008 35.929 23837 Z= 0.405 Chirality : 0.105 2.379 2714 Planarity : 0.004 0.061 2921 Dihedral : 11.703 171.775 2438 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 1.26 % Allowed : 7.65 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2047 helix: 0.17 (0.18), residues: 831 sheet: -1.54 (0.24), residues: 407 loop : -2.05 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 625 TYR 0.024 0.001 TYR F 391 PHE 0.019 0.001 PHE F 496 TRP 0.013 0.001 TRP F 368 HIS 0.004 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (17526) covalent geometry : angle 1.00689 / 0.40 (23801) hydrogen bonds : bond 0.04895 / 3.17 ( 744) hydrogen bonds : angle 4.72807 / 3.35 ( 2145) link_ALPHA1-2 : bond 0.00337 / 0.17 ( 2) link_ALPHA1-2 : angle 2.17505 / 1.36 ( 6) link_ALPHA1-3 : bond 0.00474 / 0.25 ( 1) link_ALPHA1-3 : angle 1.61317 / 0.89 ( 3) link_ALPHA1-6 : bond 0.00606 / 0.32 ( 1) link_ALPHA1-6 : angle 2.02582 / 1.17 ( 3) link_BETA1-4 : bond 0.00202 / 0.10 ( 3) link_BETA1-4 : angle 1.85916 / 1.11 ( 9) link_NAG-ASN : bond 0.00190 / 0.09 ( 5) link_NAG-ASN : angle 1.47214 / 0.80 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.8480 (ptp) cc_final: 0.8211 (ptp) REVERT: B 97 GLN cc_start: 0.8857 (tt0) cc_final: 0.8656 (tt0) REVERT: F 406 MET cc_start: 0.8507 (ttm) cc_final: 0.8180 (mtp) REVERT: F 528 ASP cc_start: 0.9086 (t0) cc_final: 0.8753 (t0) REVERT: F 632 MET cc_start: 0.9147 (ttp) cc_final: 0.8573 (mtp) REVERT: G 171 ASP cc_start: 0.8299 (m-30) cc_final: 0.7517 (p0) REVERT: G 236 ASP cc_start: 0.8715 (t0) cc_final: 0.8489 (t0) REVERT: G 311 ASP cc_start: 0.7756 (t0) cc_final: 0.7475 (t0) REVERT: H 153 GLU cc_start: 0.8371 (tt0) cc_final: 0.7647 (tm-30) outliers start: 22 outliers final: 14 residues processed: 269 average time/residue: 0.1015 time to fit residues: 42.9847 Evaluate side-chains 241 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 120 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 178 optimal weight: 40.0000 chunk 138 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN A 276 GLN G 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.157751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113729 restraints weight = 20566.709| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.13 r_work: 0.2703 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17538 Z= 0.149 Angle : 0.965 34.872 23837 Z= 0.384 Chirality : 0.104 2.451 2714 Planarity : 0.004 0.050 2921 Dihedral : 10.798 168.368 2438 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.88 % Allowed : 10.45 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2047 helix: 0.56 (0.18), residues: 836 sheet: -1.30 (0.25), residues: 408 loop : -1.91 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 625 TYR 0.023 0.001 TYR F 391 PHE 0.017 0.001 PHE F 587 TRP 0.012 0.001 TRP F 368 HIS 0.003 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (17526) covalent geometry : angle 0.96395 / 0.38 (23801) hydrogen bonds : bond 0.04359 / 2.83 ( 744) hydrogen bonds : angle 4.42831 / 3.15 ( 2145) link_ALPHA1-2 : bond 0.00256 / 0.13 ( 2) link_ALPHA1-2 : angle 1.83518 / 1.14 ( 6) link_ALPHA1-3 : bond 0.00449 / 0.24 ( 1) link_ALPHA1-3 : angle 1.34869 / 0.75 ( 3) link_ALPHA1-6 : bond 0.00119 / 0.06 ( 1) link_ALPHA1-6 : angle 1.56675 / 0.90 ( 3) link_BETA1-4 : bond 0.00269 / 0.14 ( 3) link_BETA1-4 : angle 1.69651 / 1.00 ( 9) link_NAG-ASN : bond 0.00197 / 0.10 ( 5) link_NAG-ASN : angle 1.46977 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.525 Fit side-chains REVERT: A 150 MET cc_start: 0.8554 (ptp) cc_final: 0.8267 (ptp) REVERT: B 97 GLN cc_start: 0.8884 (tt0) cc_final: 0.8564 (tt0) REVERT: F 406 MET cc_start: 0.8325 (ttm) cc_final: 0.8014 (mtp) REVERT: F 430 ASP cc_start: 0.7456 (t70) cc_final: 0.7254 (t0) REVERT: F 528 ASP cc_start: 0.9107 (t0) cc_final: 0.8755 (t0) REVERT: F 632 MET cc_start: 0.9152 (ttp) cc_final: 0.8619 (mtp) REVERT: G 97 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8114 (mmmt) REVERT: G 171 ASP cc_start: 0.8297 (m-30) cc_final: 0.7453 (p0) REVERT: G 240 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8505 (m110) REVERT: G 311 ASP cc_start: 0.7754 (t0) cc_final: 0.7433 (t0) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 0.1082 time to fit residues: 43.1159 Evaluate side-chains 244 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN A 434 GLN F 288 GLN G 377 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109046 restraints weight = 20510.957| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.11 r_work: 0.2708 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 17538 Z= 0.274 Angle : 1.027 35.533 23837 Z= 0.421 Chirality : 0.105 2.419 2714 Planarity : 0.004 0.048 2921 Dihedral : 10.691 168.080 2438 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.63 % Allowed : 12.44 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 2047 helix: 0.52 (0.18), residues: 834 sheet: -1.30 (0.26), residues: 402 loop : -1.89 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 625 TYR 0.030 0.002 TYR F 391 PHE 0.029 0.002 PHE F 587 TRP 0.012 0.001 TRP F 368 HIS 0.007 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.27 (17526) covalent geometry : angle 1.02509 / 0.42 (23801) hydrogen bonds : bond 0.05246 / 3.44 ( 744) hydrogen bonds : angle 4.55869 / 3.24 ( 2145) link_ALPHA1-2 : bond 0.00321 / 0.16 ( 2) link_ALPHA1-2 : angle 1.76144 / 1.12 ( 6) link_ALPHA1-3 : bond 0.00238 / 0.13 ( 1) link_ALPHA1-3 : angle 1.45311 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00006 / 0.00 ( 1) link_ALPHA1-6 : angle 1.65011 / 0.95 ( 3) link_BETA1-4 : bond 0.00284 / 0.14 ( 3) link_BETA1-4 : angle 2.04844 / 1.21 ( 9) link_NAG-ASN : bond 0.00329 / 0.18 ( 5) link_NAG-ASN : angle 1.86754 / 1.00 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.404 Fit side-chains REVERT: A 134 LYS cc_start: 0.8244 (mttt) cc_final: 0.7984 (mtpt) REVERT: A 150 MET cc_start: 0.8845 (ptp) cc_final: 0.8477 (ptp) REVERT: F 378 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8138 (t80) REVERT: F 406 MET cc_start: 0.8408 (ttm) cc_final: 0.8069 (mtp) REVERT: F 528 ASP cc_start: 0.9187 (t0) cc_final: 0.8986 (t0) REVERT: G 97 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8199 (mmmt) REVERT: G 171 ASP cc_start: 0.8349 (m-30) cc_final: 0.7578 (p0) REVERT: G 311 ASP cc_start: 0.7837 (t0) cc_final: 0.7576 (t0) REVERT: G 345 ILE cc_start: 0.9266 (mm) cc_final: 0.8840 (mm) REVERT: H 155 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7277 (mp) outliers start: 46 outliers final: 38 residues processed: 264 average time/residue: 0.1063 time to fit residues: 43.6154 Evaluate side-chains 264 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 594 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain H residue 91 ASN Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN G 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114069 restraints weight = 20545.600| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.12 r_work: 0.2736 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17538 Z= 0.201 Angle : 0.981 34.912 23837 Z= 0.394 Chirality : 0.104 2.360 2714 Planarity : 0.004 0.047 2921 Dihedral : 10.272 166.597 2438 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.20 % Allowed : 13.41 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.18), residues: 2047 helix: 0.66 (0.18), residues: 834 sheet: -1.23 (0.26), residues: 402 loop : -1.84 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 619 TYR 0.023 0.001 TYR F 391 PHE 0.021 0.002 PHE F 587 TRP 0.014 0.001 TRP F 368 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (17526) covalent geometry : angle 0.97944 / 0.39 (23801) hydrogen bonds : bond 0.04660 / 3.05 ( 744) hydrogen bonds : angle 4.41947 / 3.14 ( 2145) link_ALPHA1-2 : bond 0.00187 / 0.09 ( 2) link_ALPHA1-2 : angle 1.76756 / 1.11 ( 6) link_ALPHA1-3 : bond 0.00328 / 0.17 ( 1) link_ALPHA1-3 : angle 1.37395 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00037 / 0.02 ( 1) link_ALPHA1-6 : angle 1.60921 / 0.93 ( 3) link_BETA1-4 : bond 0.00230 / 0.11 ( 3) link_BETA1-4 : angle 1.75579 / 1.03 ( 9) link_NAG-ASN : bond 0.00202 / 0.11 ( 5) link_NAG-ASN : angle 1.71863 / 0.90 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.490 Fit side-chains REVERT: A 93 ASN cc_start: 0.8221 (t0) cc_final: 0.7986 (t0) REVERT: A 134 LYS cc_start: 0.8186 (mttt) cc_final: 0.7837 (mtpt) REVERT: A 150 MET cc_start: 0.8799 (ptp) cc_final: 0.8397 (ptp) REVERT: A 378 GLU cc_start: 0.8115 (tp30) cc_final: 0.7867 (tp30) REVERT: F 378 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8141 (t80) REVERT: F 406 MET cc_start: 0.8329 (ttm) cc_final: 0.8082 (mtp) REVERT: F 528 ASP cc_start: 0.9172 (t0) cc_final: 0.8965 (t0) REVERT: F 632 MET cc_start: 0.9103 (ttp) cc_final: 0.8587 (mtp) REVERT: G 97 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8209 (mmmt) REVERT: G 106 GLU cc_start: 0.8640 (mp0) cc_final: 0.8066 (mt-10) REVERT: G 171 ASP cc_start: 0.8355 (m-30) cc_final: 0.7613 (p0) REVERT: G 311 ASP cc_start: 0.7787 (t0) cc_final: 0.7514 (t0) REVERT: G 382 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: H 155 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 56 outliers final: 40 residues processed: 275 average time/residue: 0.1057 time to fit residues: 45.9373 Evaluate side-chains 264 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 594 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain H residue 91 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN H 76 ASN H 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.154627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110527 restraints weight = 20400.624| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.07 r_work: 0.2648 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17538 Z= 0.179 Angle : 0.972 34.653 23837 Z= 0.388 Chirality : 0.103 2.310 2714 Planarity : 0.004 0.045 2921 Dihedral : 9.944 165.662 2438 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.25 % Allowed : 14.61 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2047 helix: 0.79 (0.18), residues: 828 sheet: -1.14 (0.27), residues: 392 loop : -1.79 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 619 TYR 0.020 0.001 TYR F 391 PHE 0.019 0.001 PHE F 587 TRP 0.013 0.001 TRP F 368 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (17526) covalent geometry : angle 0.97104 / 0.39 (23801) hydrogen bonds : bond 0.04447 / 2.91 ( 744) hydrogen bonds : angle 4.33534 / 3.08 ( 2145) link_ALPHA1-2 : bond 0.00181 / 0.09 ( 2) link_ALPHA1-2 : angle 1.72564 / 1.08 ( 6) link_ALPHA1-3 : bond 0.00352 / 0.19 ( 1) link_ALPHA1-3 : angle 1.35857 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00063 / 0.03 ( 1) link_ALPHA1-6 : angle 1.60800 / 0.92 ( 3) link_BETA1-4 : bond 0.00237 / 0.12 ( 3) link_BETA1-4 : angle 1.72488 / 1.01 ( 9) link_NAG-ASN : bond 0.00182 / 0.10 ( 5) link_NAG-ASN : angle 1.64690 / 0.86 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 0.505 Fit side-chains REVERT: A 93 ASN cc_start: 0.8202 (t0) cc_final: 0.7967 (t0) REVERT: A 134 LYS cc_start: 0.8184 (mttt) cc_final: 0.7819 (mtpt) REVERT: A 150 MET cc_start: 0.8783 (ptp) cc_final: 0.8381 (ptp) REVERT: A 378 GLU cc_start: 0.8185 (tp30) cc_final: 0.7922 (tp30) REVERT: F 378 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8113 (t80) REVERT: F 406 MET cc_start: 0.8274 (ttm) cc_final: 0.8066 (mtp) REVERT: F 528 ASP cc_start: 0.9181 (t0) cc_final: 0.8975 (t0) REVERT: F 632 MET cc_start: 0.9117 (ttp) cc_final: 0.8618 (mtp) REVERT: G 97 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8193 (mmmt) REVERT: G 171 ASP cc_start: 0.8331 (m-30) cc_final: 0.7625 (p0) REVERT: G 196 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8231 (mtp180) REVERT: G 234 SER cc_start: 0.9008 (t) cc_final: 0.8557 (m) REVERT: G 311 ASP cc_start: 0.7826 (t0) cc_final: 0.7490 (t0) REVERT: G 381 ASP cc_start: 0.8173 (t70) cc_final: 0.7757 (t0) REVERT: G 382 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: H 99 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7586 (tm-30) REVERT: H 155 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7386 (mp) outliers start: 57 outliers final: 46 residues processed: 267 average time/residue: 0.1031 time to fit residues: 43.6973 Evaluate side-chains 274 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 594 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN A 276 GLN F 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113567 restraints weight = 20316.207| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.13 r_work: 0.2751 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17538 Z= 0.125 Angle : 0.943 33.958 23837 Z= 0.371 Chirality : 0.102 2.256 2714 Planarity : 0.004 0.045 2921 Dihedral : 9.489 164.652 2438 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.74 % Allowed : 15.70 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 2047 helix: 1.05 (0.19), residues: 825 sheet: -1.08 (0.26), residues: 392 loop : -1.70 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 619 TYR 0.016 0.001 TYR F 231 PHE 0.015 0.001 PHE G 344 TRP 0.014 0.001 TRP F 368 HIS 0.003 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17526) covalent geometry : angle 0.94200 / 0.37 (23801) hydrogen bonds : bond 0.03887 / 2.53 ( 744) hydrogen bonds : angle 4.18076 / 2.97 ( 2145) link_ALPHA1-2 : bond 0.00028 / 0.01 ( 2) link_ALPHA1-2 : angle 1.72406 / 1.07 ( 6) link_ALPHA1-3 : bond 0.00253 / 0.13 ( 1) link_ALPHA1-3 : angle 1.25857 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00175 / 0.09 ( 1) link_ALPHA1-6 : angle 1.56153 / 0.89 ( 3) link_BETA1-4 : bond 0.00286 / 0.14 ( 3) link_BETA1-4 : angle 1.54441 / 0.90 ( 9) link_NAG-ASN : bond 0.00160 / 0.08 ( 5) link_NAG-ASN : angle 1.44388 / 0.75 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.429 Fit side-chains REVERT: A 57 ASN cc_start: 0.8122 (t0) cc_final: 0.7892 (t0) REVERT: A 93 ASN cc_start: 0.8196 (t0) cc_final: 0.7965 (t0) REVERT: A 134 LYS cc_start: 0.8196 (mttt) cc_final: 0.7822 (mtpt) REVERT: A 150 MET cc_start: 0.8672 (ptp) cc_final: 0.8330 (ptp) REVERT: A 370 PRO cc_start: 0.9007 (Cg_exo) cc_final: 0.8780 (Cg_endo) REVERT: A 378 GLU cc_start: 0.8151 (tp30) cc_final: 0.7858 (tp30) REVERT: F 378 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8065 (t80) REVERT: F 406 MET cc_start: 0.8227 (ttm) cc_final: 0.8004 (mtp) REVERT: F 528 ASP cc_start: 0.9195 (t0) cc_final: 0.8889 (t0) REVERT: F 614 TYR cc_start: 0.8924 (t80) cc_final: 0.8409 (t80) REVERT: F 632 MET cc_start: 0.9133 (ttp) cc_final: 0.8666 (mtp) REVERT: G 97 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8179 (mmmt) REVERT: G 171 ASP cc_start: 0.8325 (m-30) cc_final: 0.7654 (p0) REVERT: G 234 SER cc_start: 0.9001 (t) cc_final: 0.8583 (m) REVERT: G 311 ASP cc_start: 0.7824 (t0) cc_final: 0.7501 (t0) REVERT: G 382 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: H 99 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7589 (tm-30) REVERT: H 155 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7332 (mp) outliers start: 48 outliers final: 36 residues processed: 260 average time/residue: 0.1197 time to fit residues: 48.2483 Evaluate side-chains 258 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099528 restraints weight = 20277.542| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.20 r_work: 0.2692 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17538 Z= 0.141 Angle : 0.946 33.988 23837 Z= 0.373 Chirality : 0.102 2.234 2714 Planarity : 0.004 0.045 2921 Dihedral : 9.278 164.588 2438 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.85 % Allowed : 16.04 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 2047 helix: 1.12 (0.19), residues: 824 sheet: -1.05 (0.27), residues: 392 loop : -1.68 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 196 TYR 0.016 0.001 TYR F 391 PHE 0.017 0.001 PHE G 344 TRP 0.013 0.001 TRP F 368 HIS 0.004 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (17526) covalent geometry : angle 0.94525 / 0.37 (23801) hydrogen bonds : bond 0.03945 / 2.58 ( 744) hydrogen bonds : angle 4.15576 / 2.95 ( 2145) link_ALPHA1-2 : bond 0.00102 / 0.05 ( 2) link_ALPHA1-2 : angle 1.67751 / 1.05 ( 6) link_ALPHA1-3 : bond 0.00371 / 0.20 ( 1) link_ALPHA1-3 : angle 1.30794 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00144 / 0.08 ( 1) link_ALPHA1-6 : angle 1.56010 / 0.89 ( 3) link_BETA1-4 : bond 0.00275 / 0.14 ( 3) link_BETA1-4 : angle 1.63111 / 0.95 ( 9) link_NAG-ASN : bond 0.00138 / 0.07 ( 5) link_NAG-ASN : angle 1.44478 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.665 Fit side-chains REVERT: A 57 ASN cc_start: 0.8233 (t0) cc_final: 0.7990 (t0) REVERT: A 93 ASN cc_start: 0.8156 (t0) cc_final: 0.7881 (t0) REVERT: A 134 LYS cc_start: 0.8159 (mttt) cc_final: 0.7779 (mtpt) REVERT: A 150 MET cc_start: 0.8678 (ptp) cc_final: 0.8333 (ptp) REVERT: A 370 PRO cc_start: 0.9023 (Cg_exo) cc_final: 0.8809 (Cg_endo) REVERT: A 378 GLU cc_start: 0.8314 (tp30) cc_final: 0.8015 (tp30) REVERT: F 378 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8096 (t80) REVERT: F 406 MET cc_start: 0.8201 (ttm) cc_final: 0.7994 (mtp) REVERT: F 528 ASP cc_start: 0.9145 (t0) cc_final: 0.8928 (t0) REVERT: F 632 MET cc_start: 0.9159 (ttp) cc_final: 0.8689 (mtp) REVERT: G 97 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8149 (mmmt) REVERT: G 171 ASP cc_start: 0.8263 (m-30) cc_final: 0.7612 (p0) REVERT: G 234 SER cc_start: 0.9062 (t) cc_final: 0.8636 (m) REVERT: G 311 ASP cc_start: 0.7798 (t0) cc_final: 0.7465 (t0) REVERT: G 382 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: H 99 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7620 (tm-30) REVERT: H 155 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7284 (mp) outliers start: 50 outliers final: 41 residues processed: 253 average time/residue: 0.1234 time to fit residues: 49.2893 Evaluate side-chains 261 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 425 PHE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 178 optimal weight: 40.0000 chunk 112 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 111 optimal weight: 0.0970 chunk 166 optimal weight: 0.0000 chunk 97 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.146300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101428 restraints weight = 20172.000| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.21 r_work: 0.2720 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17538 Z= 0.107 Angle : 0.932 33.439 23837 Z= 0.365 Chirality : 0.102 2.199 2714 Planarity : 0.004 0.045 2921 Dihedral : 9.022 164.445 2438 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.57 % Allowed : 16.15 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 2047 helix: 1.30 (0.19), residues: 824 sheet: -0.97 (0.26), residues: 397 loop : -1.62 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 619 TYR 0.015 0.001 TYR F 231 PHE 0.016 0.001 PHE F 284 TRP 0.014 0.001 TRP F 368 HIS 0.004 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17526) covalent geometry : angle 0.93073 / 0.36 (23801) hydrogen bonds : bond 0.03560 / 2.32 ( 744) hydrogen bonds : angle 4.04642 / 2.87 ( 2145) link_ALPHA1-2 : bond 0.00046 / 0.02 ( 2) link_ALPHA1-2 : angle 1.66238 / 1.03 ( 6) link_ALPHA1-3 : bond 0.00421 / 0.22 ( 1) link_ALPHA1-3 : angle 1.27712 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00263 / 0.14 ( 1) link_ALPHA1-6 : angle 1.53946 / 0.88 ( 3) link_BETA1-4 : bond 0.00287 / 0.14 ( 3) link_BETA1-4 : angle 1.49066 / 0.87 ( 9) link_NAG-ASN : bond 0.00188 / 0.10 ( 5) link_NAG-ASN : angle 1.34354 / 0.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.653 Fit side-chains REVERT: A 57 ASN cc_start: 0.8234 (t0) cc_final: 0.7998 (t0) REVERT: A 93 ASN cc_start: 0.8111 (t0) cc_final: 0.7814 (t0) REVERT: A 134 LYS cc_start: 0.8129 (mttt) cc_final: 0.7752 (mtpt) REVERT: A 150 MET cc_start: 0.8529 (ptp) cc_final: 0.8254 (ptp) REVERT: A 378 GLU cc_start: 0.8297 (tp30) cc_final: 0.8009 (tp30) REVERT: F 378 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8066 (t80) REVERT: F 406 MET cc_start: 0.8115 (ttm) cc_final: 0.7904 (mtp) REVERT: F 528 ASP cc_start: 0.9106 (t0) cc_final: 0.8795 (t0) REVERT: F 614 TYR cc_start: 0.8911 (t80) cc_final: 0.8488 (t80) REVERT: F 632 MET cc_start: 0.9194 (ttp) cc_final: 0.8728 (mtp) REVERT: G 97 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8109 (mmmt) REVERT: G 171 ASP cc_start: 0.8220 (m-30) cc_final: 0.7583 (p0) REVERT: G 234 SER cc_start: 0.9077 (t) cc_final: 0.8663 (m) REVERT: G 311 ASP cc_start: 0.7849 (t0) cc_final: 0.7499 (t0) REVERT: G 382 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: H 99 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7601 (tm-30) REVERT: H 150 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7853 (pt) REVERT: H 155 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7215 (mp) outliers start: 45 outliers final: 34 residues processed: 260 average time/residue: 0.1246 time to fit residues: 51.4700 Evaluate side-chains 262 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 425 PHE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 173 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 174 optimal weight: 0.0470 chunk 6 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.148431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.104365 restraints weight = 20255.531| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.38 r_work: 0.2702 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17538 Z= 0.122 Angle : 0.935 33.510 23837 Z= 0.366 Chirality : 0.102 2.184 2714 Planarity : 0.004 0.045 2921 Dihedral : 8.881 165.185 2438 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 16.27 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 2047 helix: 1.34 (0.19), residues: 825 sheet: -0.97 (0.26), residues: 395 loop : -1.60 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 619 TYR 0.015 0.001 TYR F 391 PHE 0.017 0.001 PHE H 79 TRP 0.013 0.001 TRP F 368 HIS 0.004 0.001 HIS F 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17526) covalent geometry : angle 0.93443 / 0.37 (23801) hydrogen bonds : bond 0.03642 / 2.38 ( 744) hydrogen bonds : angle 4.03183 / 2.86 ( 2145) link_ALPHA1-2 : bond 0.00071 / 0.04 ( 2) link_ALPHA1-2 : angle 1.61909 / 1.01 ( 6) link_ALPHA1-3 : bond 0.00359 / 0.19 ( 1) link_ALPHA1-3 : angle 1.29715 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00144 / 0.08 ( 1) link_ALPHA1-6 : angle 1.50174 / 0.86 ( 3) link_BETA1-4 : bond 0.00290 / 0.15 ( 3) link_BETA1-4 : angle 1.56012 / 0.91 ( 9) link_NAG-ASN : bond 0.00172 / 0.09 ( 5) link_NAG-ASN : angle 1.33757 / 0.69 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.601 Fit side-chains REVERT: A 57 ASN cc_start: 0.8247 (t0) cc_final: 0.7999 (t0) REVERT: A 93 ASN cc_start: 0.8133 (t0) cc_final: 0.7842 (t0) REVERT: A 134 LYS cc_start: 0.8177 (mttt) cc_final: 0.7805 (mtpt) REVERT: A 150 MET cc_start: 0.8539 (ptp) cc_final: 0.8284 (ptp) REVERT: A 378 GLU cc_start: 0.8345 (tp30) cc_final: 0.8041 (tp30) REVERT: F 378 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8080 (t80) REVERT: F 406 MET cc_start: 0.8173 (ttm) cc_final: 0.7950 (mtp) REVERT: F 528 ASP cc_start: 0.9126 (t0) cc_final: 0.8826 (t0) REVERT: F 614 TYR cc_start: 0.8910 (t80) cc_final: 0.8508 (t80) REVERT: F 632 MET cc_start: 0.9161 (ttp) cc_final: 0.8720 (mtp) REVERT: F 654 MET cc_start: 0.8113 (mmt) cc_final: 0.7891 (mmp) REVERT: G 35 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7335 (mm-30) REVERT: G 97 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8120 (mmmt) REVERT: G 171 ASP cc_start: 0.8240 (m-30) cc_final: 0.7674 (p0) REVERT: G 311 ASP cc_start: 0.7859 (t0) cc_final: 0.7506 (t0) REVERT: G 382 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: H 99 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7618 (tm-30) REVERT: H 150 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7822 (pt) REVERT: H 155 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7197 (mp) outliers start: 43 outliers final: 34 residues processed: 256 average time/residue: 0.1255 time to fit residues: 50.7644 Evaluate side-chains 262 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 425 PHE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 0.0870 chunk 141 optimal weight: 8.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.135590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.089722 restraints weight = 20843.835| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.22 r_work: 0.2604 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 17538 Z= 0.351 Angle : 1.062 35.491 23837 Z= 0.443 Chirality : 0.104 2.230 2714 Planarity : 0.004 0.048 2921 Dihedral : 9.594 168.444 2438 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.40 % Allowed : 16.89 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2047 helix: 0.75 (0.18), residues: 828 sheet: -1.24 (0.26), residues: 398 loop : -1.74 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 619 TYR 0.027 0.002 TYR F 391 PHE 0.033 0.002 PHE F 587 TRP 0.013 0.002 TRP F 356 HIS 0.007 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.35 (17526) covalent geometry : angle 1.05961 / 0.44 (23801) hydrogen bonds : bond 0.05556 / 3.67 ( 744) hydrogen bonds : angle 4.51394 / 3.21 ( 2145) link_ALPHA1-2 : bond 0.00216 / 0.10 ( 2) link_ALPHA1-2 : angle 1.67753 / 1.08 ( 6) link_ALPHA1-3 : bond 0.00080 / 0.04 ( 1) link_ALPHA1-3 : angle 1.48916 / 0.84 ( 3) link_ALPHA1-6 : bond 0.00066 / 0.03 ( 1) link_ALPHA1-6 : angle 1.65271 / 0.95 ( 3) link_BETA1-4 : bond 0.00287 / 0.14 ( 3) link_BETA1-4 : angle 2.27769 / 1.34 ( 9) link_NAG-ASN : bond 0.00408 / 0.22 ( 5) link_NAG-ASN : angle 2.14071 / 1.14 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.09 seconds wall clock time: 73 minutes 4.18 seconds (4384.18 seconds total)