Starting phenix.real_space_refine on Thu Aug 6 13:29:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ydm_39177/08_2026/8ydm_39177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ydm_39177/08_2026/8ydm_39177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ydm_39177/08_2026/8ydm_39177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ydm_39177/08_2026/8ydm_39177.map" model { file = "/net/cci-nas-00/data/ceres_data/8ydm_39177/08_2026/8ydm_39177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ydm_39177/08_2026/8ydm_39177.cif" } resolution = 3.05 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= 0.005 sd= 0.065 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: 8 Type Number sf(0) Gaussians Mn 1 7.51 5 Fe 4 7.16 5 P 1 5.49 5 Mg 24 5.21 5 S 36 5.16 5 C 10818 2.51 5 N 2310 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15637 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 314 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 370 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "C" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3155 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 27, 'TRANS': 379} Chain: "D" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 289 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "F" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "G" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 416 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 43} Chain: "H" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 293 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "I" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 423 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 289 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "K" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "L" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2463 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 21, 'TRANS': 284} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2404 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 18, 'TRANS': 276} Chain: "N" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 421 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "O" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "P" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 289 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "R" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 3, 'U4Z': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'U4Z': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 217 Unusual residues: {'HEM': 4, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'BCL': 2, 'U4Z': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCL': 2, 'U4Z': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0001': 1, 'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'BCL': 2, 'U4Z': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2, 'BCL:plan_0001': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'BCL': 2, 'U4Z': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 194 Unusual residues: {'BCL': 1, 'BPH': 1, 'MQE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'MQE:plan-12': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 307 Unusual residues: {' MN': 1, 'BCL': 2, 'BPH': 2, 'MQE': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'MQE:plan-12': 1, 'BPH:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCL': 2, 'U4Z': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCL': 1, 'U4Z': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'BCL': 1, 'U4Z': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'BCL': 2, 'U4Z': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2, 'BCL:plan_0001': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 3.55, per 1000 atoms: 0.23 Number of scatterers: 15637 At special positions: 0 Unit cell: (128.182, 106.256, 116.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 Mn 1 24.99 S 36 16.00 P 1 15.00 Mg 24 11.99 O 2443 8.00 N 2310 7.00 C 10818 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 635.3 milliseconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3078 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 7 sheets defined 65.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'B' and resid 19 through 47 removed outlier: 3.808A pdb=" N HIS B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 50 removed outlier: 4.357A pdb=" N VAL C 14 " --> pdb=" O GLN C 10 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 4.094A pdb=" N GLY C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 98 Processing helix chain 'C' and resid 111 through 123 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.711A pdb=" N LEU C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 removed outlier: 3.658A pdb=" N TYR C 133 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS C 134 " --> pdb=" O CYS C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 134' Processing helix chain 'C' and resid 145 through 166 removed outlier: 3.861A pdb=" N ILE C 149 " --> pdb=" O TYR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.735A pdb=" N HIS C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 273 through 291 removed outlier: 4.081A pdb=" N THR C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.684A pdb=" N CYS C 297 " --> pdb=" O CYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 341 removed outlier: 3.511A pdb=" N THR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 377 through 383 removed outlier: 4.143A pdb=" N CYS C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 382 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.975A pdb=" N VAL C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.515A pdb=" N ARG C 412 " --> pdb=" O PRO C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 32 removed outlier: 3.695A pdb=" N SER D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 removed outlier: 3.661A pdb=" N ARG E 13 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 47 removed outlier: 3.618A pdb=" N LEU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 32 removed outlier: 3.732A pdb=" N ILE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY F 18 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 40 removed outlier: 3.787A pdb=" N SER F 39 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN F 40 " --> pdb=" O TRP F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 36 through 40' Processing helix chain 'G' and resid 17 through 49 Processing helix chain 'H' and resid 6 through 31 removed outlier: 4.535A pdb=" N VAL H 12 " --> pdb=" O ARG H 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 33 removed outlier: 3.509A pdb=" N LEU I 23 " --> pdb=" O GLN I 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 47 removed outlier: 3.570A pdb=" N ALA I 39 " --> pdb=" O GLY I 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 32 removed outlier: 4.013A pdb=" N LEU J 30 " --> pdb=" O HIS J 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 17 through 49 removed outlier: 3.950A pdb=" N LEU K 23 " --> pdb=" O GLN K 19 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL K 28 " --> pdb=" O HIS K 24 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 40 Proline residue: L 38 - end of helix Processing helix chain 'L' and resid 67 through 87 Processing helix chain 'L' and resid 95 through 103 removed outlier: 4.639A pdb=" N PHE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 123 through 151 Processing helix chain 'L' and resid 155 through 173 Processing helix chain 'L' and resid 173 through 180 Processing helix chain 'L' and resid 189 through 203 removed outlier: 4.725A pdb=" N GLY L 201 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 209 Processing helix chain 'L' and resid 210 through 238 Processing helix chain 'L' and resid 247 through 257 Processing helix chain 'L' and resid 262 through 288 removed outlier: 3.779A pdb=" N HIS L 267 " --> pdb=" O GLU L 263 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY L 277 " --> pdb=" O PHE L 273 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE L 278 " --> pdb=" O ALA L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 303 removed outlier: 3.645A pdb=" N TRP L 299 " --> pdb=" O VAL L 296 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE L 301 " --> pdb=" O PHE L 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 33 removed outlier: 3.969A pdb=" N ASN M 31 " --> pdb=" O PRO M 27 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE M 32 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 69 removed outlier: 3.577A pdb=" N GLN M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL M 69 " --> pdb=" O MET M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 80 Processing helix chain 'M' and resid 102 through 130 Processing helix chain 'M' and resid 134 through 152 removed outlier: 3.508A pdb=" N TYR M 138 " --> pdb=" O PRO M 134 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY M 142 " --> pdb=" O TYR M 138 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA M 143 " --> pdb=" O GLY M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 159 Processing helix chain 'M' and resid 160 through 164 removed outlier: 3.746A pdb=" N GLU M 163 " --> pdb=" O ASP M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 183 removed outlier: 4.100A pdb=" N LEU M 173 " --> pdb=" O ILE M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 188 Processing helix chain 'M' and resid 189 through 216 Processing helix chain 'M' and resid 217 through 220 Processing helix chain 'M' and resid 223 through 230 removed outlier: 3.919A pdb=" N GLN M 229 " --> pdb=" O TRP M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 247 removed outlier: 3.890A pdb=" N THR M 235 " --> pdb=" O PRO M 231 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 238 " --> pdb=" O GLY M 234 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE M 241 " --> pdb=" O ARG M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 277 removed outlier: 3.668A pdb=" N HIS M 256 " --> pdb=" O ALA M 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS M 266 " --> pdb=" O PHE M 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY M 267 " --> pdb=" O ALA M 263 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE M 268 " --> pdb=" O TRP M 264 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY M 270 " --> pdb=" O CYS M 266 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY M 273 " --> pdb=" O THR M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 293 Processing helix chain 'N' and resid 16 through 42 Processing helix chain 'O' and resid 7 through 32 removed outlier: 3.544A pdb=" N PHE O 14 " --> pdb=" O ASN O 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY O 18 " --> pdb=" O PHE O 14 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 49 removed outlier: 4.437A pdb=" N VAL P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL P 28 " --> pdb=" O HIS P 24 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 32 Processing helix chain 'R' and resid 9 through 13 removed outlier: 3.532A pdb=" N ARG R 13 " --> pdb=" O PRO R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 47 removed outlier: 3.584A pdb=" N ILE R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 175 through 176 Processing sheet with id=AA2, first strand: chain 'C' and resid 205 through 206 Processing sheet with id=AA3, first strand: chain 'C' and resid 247 through 249 Processing sheet with id=AA4, first strand: chain 'C' and resid 364 through 366 Processing sheet with id=AA5, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AA6, first strand: chain 'M' and resid 24 through 25 Processing sheet with id=AA7, first strand: chain 'N' and resid 46 through 47 762 hydrogen bonds defined for protein. 2211 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: 2.65 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.31: 2257 1.31 - 1.53: 12141 1.53 - 1.74: 1782 1.74 - 1.96: 102 1.96 - 2.18: 68 Bond restraints: 16350 Sorted by residual: bond pdb=" CAD U4Z R 101 " pdb=" CAH U4Z R 101 " ideal model delta sigma weight residual 1.346 1.537 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" CAD U4Z G 101 " pdb=" CAH U4Z G 101 " ideal model delta sigma weight residual 1.346 1.533 -0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" CAD U4Z I 101 " pdb=" CAH U4Z I 101 " ideal model delta sigma weight residual 1.346 1.526 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" CAD U4Z D 104 " pdb=" CAH U4Z D 104 " ideal model delta sigma weight residual 1.346 1.515 -0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C ASN L 250 " pdb=" O ASN L 250 " ideal model delta sigma weight residual 1.236 1.134 0.102 1.22e-02 6.72e+03 7.00e+01 ... (remaining 16345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.79: 22685 14.79 - 29.58: 85 29.58 - 44.37: 21 44.37 - 59.16: 1 59.16 - 73.95: 1 Bond angle restraints: 22793 Sorted by residual: angle pdb=" CBC U4Z A 102 " pdb=" CAY U4Z A 102 " pdb=" CBD U4Z A 102 " ideal model delta sigma weight residual 114.38 40.43 73.95 3.00e+00 1.11e-01 6.08e+02 angle pdb=" CAU U4Z I 101 " pdb=" CAR U4Z I 101 " pdb=" CAV U4Z I 101 " ideal model delta sigma weight residual 123.73 76.35 47.38 3.00e+00 1.11e-01 2.49e+02 angle pdb=" C1C BCL O 103 " pdb=" C2C BCL O 103 " pdb=" CMC BCL O 103 " ideal model delta sigma weight residual 113.11 73.07 40.04 2.93e+00 1.16e-01 1.86e+02 angle pdb=" N PRO P 9 " pdb=" CA PRO P 9 " pdb=" C PRO P 9 " ideal model delta sigma weight residual 110.70 127.22 -16.52 1.22e+00 6.72e-01 1.83e+02 angle pdb=" CBE U4Z D 104 " pdb=" CBF U4Z D 104 " pdb=" CBH U4Z D 104 " ideal model delta sigma weight residual 125.97 165.11 -39.14 3.00e+00 1.11e-01 1.70e+02 ... (remaining 22788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 8226 35.52 - 71.03: 471 71.03 - 106.55: 117 106.55 - 142.06: 37 142.06 - 177.58: 6 Dihedral angle restraints: 8857 sinusoidal: 4062 harmonic: 4795 Sorted by residual: dihedral pdb=" CBD BCL G 103 " pdb=" CGD BCL G 103 " pdb=" O2D BCL G 103 " pdb=" CED BCL G 103 " ideal model delta sinusoidal sigma weight residual 180.00 47.44 132.56 1 5.00e+00 4.00e-02 6.44e+02 dihedral pdb=" C1 BCL P 102 " pdb=" CGA BCL P 102 " pdb=" O2A BCL P 102 " pdb=" CBA BCL P 102 " ideal model delta sinusoidal sigma weight residual -180.00 -36.81 -143.19 1 6.00e+00 2.78e-02 4.80e+02 dihedral pdb=" C1 BCL J 101 " pdb=" CGA BCL J 101 " pdb=" O2A BCL J 101 " pdb=" CBA BCL J 101 " ideal model delta sinusoidal sigma weight residual -180.00 -55.00 -125.00 1 6.00e+00 2.78e-02 4.20e+02 ... (remaining 8854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.060: 2202 1.060 - 2.120: 0 2.120 - 3.179: 0 3.179 - 4.239: 0 4.239 - 5.299: 4 Chirality restraints: 2206 Sorted by residual: chirality pdb=" C13 BPH M 401 " pdb=" C12 BPH M 401 " pdb=" C14 BPH M 401 " pdb=" C15 BPH M 401 " both_signs ideal model delta sigma weight residual False 2.60 -2.70 5.30 2.00e-01 2.50e+01 7.02e+02 chirality pdb=" C8 BPH L 403 " pdb=" C10 BPH L 403 " pdb=" C7 BPH L 403 " pdb=" C9 BPH L 403 " both_signs ideal model delta sigma weight residual False 2.55 -2.75 5.30 2.00e-01 2.50e+01 7.02e+02 chirality pdb=" C13 BPH L 403 " pdb=" C12 BPH L 403 " pdb=" C14 BPH L 403 " pdb=" C15 BPH L 403 " both_signs ideal model delta sigma weight residual False 2.60 -2.54 5.14 2.00e-01 2.50e+01 6.61e+02 ... (remaining 2203 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3D BCL A 104 " -0.044 5.00e-03 4.00e+04 7.90e-02 9.99e+02 pdb=" CAD BCL A 104 " 0.136 5.00e-03 4.00e+04 pdb=" CBD BCL A 104 " -0.036 5.00e-03 4.00e+04 pdb=" OBD BCL A 104 " -0.057 5.00e-03 4.00e+04 delta sigma weight rms_deltas residual plane pdb=" C3D BCL I 104 " 0.043 5.00e-03 4.00e+04 7.86e-02 9.88e+02 pdb=" CAD BCL I 104 " -0.135 5.00e-03 4.00e+04 pdb=" CBD BCL I 104 " 0.036 5.00e-03 4.00e+04 pdb=" OBD BCL I 104 " 0.056 5.00e-03 4.00e+04 delta sigma weight rms_deltas residual plane pdb=" C3D BCL R 103 " -0.043 5.00e-03 4.00e+04 7.83e-02 9.81e+02 pdb=" CAD BCL R 103 " 0.135 5.00e-03 4.00e+04 pdb=" CBD BCL R 103 " -0.036 5.00e-03 4.00e+04 pdb=" OBD BCL R 103 " -0.056 5.00e-03 4.00e+04 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 44 2.38 - 3.01: 8421 3.01 - 3.64: 23961 3.64 - 4.27: 36348 4.27 - 4.90: 61119 Nonbonded interactions: 129893 Sorted by model distance: nonbonded pdb=" OE2 GLU M 224 " pdb="MN MN M 404 " model vdw 1.744 2.320 nonbonded pdb=" O PHE O 14 " pdb=" O LEU O 17 " model vdw 1.796 3.040 nonbonded pdb=" O05 PGV C 505 " pdb=" O13 PGV C 505 " model vdw 2.039 3.040 nonbonded pdb=" N GLY O 18 " pdb=" N PHE O 19 " model vdw 2.078 2.560 nonbonded pdb=" OXT PRO P 53 " pdb=" CBC U4Z P 101 " model vdw 2.089 2.768 ... (remaining 129888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 40) selection = (chain 'D' and resid 6 through 40) selection = (chain 'F' and resid 6 through 40) selection = (chain 'J' and resid 6 through 40) selection = (chain 'O' and resid 6 through 40) selection = (chain 'Q' and resid 6 through 40) } ncs_group { reference = (chain 'B' and resid 10 through 52) selection = (chain 'E' and resid 10 through 52) } ncs_group { reference = (chain 'G' and (resid 5 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 101)) selection = (chain 'I' and resid 5 through 101) selection = (chain 'K' and (resid 5 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 101)) selection = (chain 'P' and (resid 5 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 101)) selection = (chain 'R' and (resid 5 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 101)) } 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=0.11 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.440 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.025 0.690 16382 Z= 1.803 Angle : 2.621 73.946 22793 Z= 1.074 Chirality : 0.246 5.299 2206 Planarity : 0.024 0.297 2858 Dihedral : 25.200 177.578 5779 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.44 % Favored : 91.76 % Rotamer: Outliers : 1.98 % Allowed : 26.03 % Favored : 71.99 % Cbeta Deviations : 0.71 % 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: -0.31 (0.21), residues: 1626 helix: 1.21 (0.17), residues: 916 sheet: -1.27 (1.44), residues: 10 loop : -2.23 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 91 TYR 0.028 0.002 TYR C 320 PHE 0.054 0.002 PHE J 14 TRP 0.022 0.001 TRP B 48 HIS 0.012 0.002 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.01952 / 0.92 (16350) covalent geometry : angle 2.62081 / 1.07 (22793) hydrogen bonds : bond 0.18058 / 11.98 ( 762) hydrogen bonds : angle 5.99265 / 4.39 ( 2211) Misc. bond : bond 0.36076 / 24.28 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7996 (mp) REVERT: C 37 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7814 (mm) REVERT: C 216 MET cc_start: 0.8024 (mpp) cc_final: 0.7398 (mmt) REVERT: G 49 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7693 (ttpt) REVERT: J 34 GLU cc_start: 0.7044 (pt0) cc_final: 0.6525 (pt0) REVERT: L 247 ASP cc_start: 0.7787 (m-30) cc_final: 0.7568 (t0) REVERT: L 304 ASN cc_start: 0.7592 (m-40) cc_final: 0.7192 (p0) REVERT: M 218 LYS cc_start: 0.7468 (mtmt) cc_final: 0.5950 (mmtt) REVERT: O 10 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7463 (m110) outliers start: 28 outliers final: 10 residues processed: 315 average time/residue: 0.1168 time to fit residues: 55.6931 Evaluate side-chains 220 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain M residue 30 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 10 ASN Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 25 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 ASN C 139 ASN ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 ASN J 10 ASN L 127 GLN M 37 GLN P 19 GLN Q 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134411 restraints weight = 25092.569| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.72 r_work: 0.3523 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.397 16382 Z= 0.181 Angle : 0.974 17.176 22793 Z= 0.405 Chirality : 0.044 0.227 2206 Planarity : 0.007 0.102 2858 Dihedral : 22.351 179.684 2833 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.01 % Favored : 92.62 % Rotamer: Outliers : 4.38 % Allowed : 22.14 % Favored : 73.48 % 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: 0.11 (0.21), residues: 1626 helix: 1.50 (0.17), residues: 929 sheet: -0.82 (1.51), residues: 10 loop : -2.04 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 91 TYR 0.027 0.001 TYR C 320 PHE 0.032 0.002 PHE Q 14 TRP 0.015 0.001 TRP B 48 HIS 0.008 0.001 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (16350) covalent geometry : angle 0.97410 / 0.41 (22793) hydrogen bonds : bond 0.05879 / 3.72 ( 762) hydrogen bonds : angle 4.76500 / 3.49 ( 2211) Misc. bond : bond 0.10956 / 7.57 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.3777 (OUTLIER) cc_final: 0.1514 (mmm160) REVERT: C 37 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7915 (mm) REVERT: C 119 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8608 (mtp) REVERT: C 216 MET cc_start: 0.8288 (mpp) cc_final: 0.7611 (mmt) REVERT: G 49 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7745 (ttpt) REVERT: I 29 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6954 (tttm) REVERT: J 8 ARG cc_start: 0.6892 (mmm-85) cc_final: 0.5390 (ptt-90) REVERT: J 34 GLU cc_start: 0.7197 (pt0) cc_final: 0.6627 (pt0) REVERT: L 59 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: L 233 LEU cc_start: 0.8745 (tp) cc_final: 0.8341 (tp) REVERT: L 247 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7591 (t0) REVERT: M 47 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7934 (p0) REVERT: M 218 LYS cc_start: 0.7794 (mtmt) cc_final: 0.6287 (mmtt) REVERT: P 8 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6485 (t) outliers start: 62 outliers final: 25 residues processed: 275 average time/residue: 0.1021 time to fit residues: 44.8389 Evaluate side-chains 235 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain L residue 285 ILE Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 14 PHE Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 24 HIS Chi-restraints excluded: chain P residue 25 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 GLN G 19 GLN M 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130177 restraints weight = 25586.631| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.77 r_work: 0.3492 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.398 16382 Z= 0.171 Angle : 0.856 17.458 22793 Z= 0.366 Chirality : 0.044 0.190 2206 Planarity : 0.006 0.095 2858 Dihedral : 19.560 179.591 2823 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer: Outliers : 5.30 % Allowed : 20.65 % Favored : 74.05 % 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: 0.33 (0.21), residues: 1626 helix: 1.61 (0.16), residues: 943 sheet: -0.59 (1.62), residues: 10 loop : -1.90 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 91 TYR 0.023 0.001 TYR C 320 PHE 0.029 0.002 PHE Q 14 TRP 0.021 0.001 TRP B 48 HIS 0.019 0.002 HIS K 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (16350) covalent geometry : angle 0.85606 / 0.37 (22793) hydrogen bonds : bond 0.04858 / 3.10 ( 762) hydrogen bonds : angle 4.38203 / 3.23 ( 2211) Misc. bond : bond 0.10640 / 7.71 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 218 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASP cc_start: 0.7427 (t0) cc_final: 0.6951 (m-30) REVERT: C 30 THR cc_start: 0.7597 (t) cc_final: 0.7309 (t) REVERT: C 37 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7937 (mm) REVERT: C 143 ASP cc_start: 0.7540 (p0) cc_final: 0.7323 (p0) REVERT: C 216 MET cc_start: 0.8539 (mpp) cc_final: 0.7830 (mmt) REVERT: D 13 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (mp) REVERT: D 23 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8645 (mt) REVERT: E 25 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6250 (t70) REVERT: G 25 ASP cc_start: 0.6668 (t0) cc_final: 0.6462 (t0) REVERT: G 49 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7925 (ttpt) REVERT: I 13 ARG cc_start: 0.7034 (tpp-160) cc_final: 0.6485 (tpp80) REVERT: I 29 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7097 (tttm) REVERT: J 8 ARG cc_start: 0.7188 (mmm-85) cc_final: 0.5424 (ptt180) REVERT: K 7 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5646 (mm) REVERT: K 49 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7030 (ptpt) REVERT: L 59 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: L 247 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7716 (t70) REVERT: M 186 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8065 (t80) REVERT: M 204 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8413 (tp) REVERT: M 218 LYS cc_start: 0.8089 (mtmt) cc_final: 0.6064 (mptt) REVERT: Q 17 LEU cc_start: 0.8046 (tp) cc_final: 0.7838 (tp) REVERT: Q 34 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7105 (tm-30) outliers start: 75 outliers final: 34 residues processed: 273 average time/residue: 0.1054 time to fit residues: 44.4189 Evaluate side-chains 245 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 186 PHE Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 24 HIS Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain Q residue 14 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 0.0000 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129246 restraints weight = 25514.817| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.83 r_work: 0.3468 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.437 16382 Z= 0.144 Angle : 0.791 16.686 22793 Z= 0.334 Chirality : 0.041 0.181 2206 Planarity : 0.005 0.087 2858 Dihedral : 18.604 179.742 2822 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.42 % Rotamer: Outliers : 4.10 % Allowed : 21.15 % Favored : 74.75 % 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: 0.65 (0.21), residues: 1626 helix: 1.89 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 91 TYR 0.019 0.001 TYR C 320 PHE 0.026 0.001 PHE Q 14 TRP 0.016 0.001 TRP B 48 HIS 0.006 0.001 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (16350) covalent geometry : angle 0.79121 / 0.33 (22793) hydrogen bonds : bond 0.04479 / 2.84 ( 762) hydrogen bonds : angle 4.22749 / 3.14 ( 2211) Misc. bond : bond 0.11668 / 8.74 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4250 (OUTLIER) cc_final: 0.2214 (mmm160) REVERT: B 22 LEU cc_start: 0.8605 (mt) cc_final: 0.8235 (mt) REVERT: B 25 ASP cc_start: 0.7384 (t0) cc_final: 0.6793 (m-30) REVERT: C 30 THR cc_start: 0.7559 (t) cc_final: 0.7331 (t) REVERT: C 37 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7889 (mm) REVERT: C 216 MET cc_start: 0.8611 (mpp) cc_final: 0.7845 (mmt) REVERT: D 13 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8261 (mp) REVERT: E 25 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6428 (t70) REVERT: G 49 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7824 (ttpt) REVERT: I 13 ARG cc_start: 0.6872 (tpp-160) cc_final: 0.6251 (tpp80) REVERT: I 29 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6976 (tttm) REVERT: J 8 ARG cc_start: 0.7227 (mmm-85) cc_final: 0.5158 (ptt-90) REVERT: L 59 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: L 77 ILE cc_start: 0.7917 (mt) cc_final: 0.7584 (tt) REVERT: L 87 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8068 (mm-30) REVERT: L 184 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7872 (mm-30) REVERT: L 247 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7781 (t70) REVERT: M 186 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8087 (t80) REVERT: M 204 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8365 (tp) REVERT: Q 17 LEU cc_start: 0.7844 (tp) cc_final: 0.7564 (tp) outliers start: 58 outliers final: 32 residues processed: 257 average time/residue: 0.1179 time to fit residues: 47.1614 Evaluate side-chains 244 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 186 PHE Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain P residue 24 HIS Chi-restraints excluded: chain P residue 25 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 128 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN M 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122641 restraints weight = 25562.746| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.77 r_work: 0.3381 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.501 16382 Z= 0.242 Angle : 0.904 20.405 22793 Z= 0.382 Chirality : 0.046 0.176 2206 Planarity : 0.006 0.080 2858 Dihedral : 18.345 179.502 2819 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.52 % Favored : 93.11 % Rotamer: Outliers : 4.67 % Allowed : 20.51 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.35 (0.21), residues: 1626 helix: 1.57 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -1.77 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 91 TYR 0.038 0.002 TYR C 320 PHE 0.030 0.002 PHE Q 14 TRP 0.018 0.001 TRP B 48 HIS 0.011 0.002 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.24 (16350) covalent geometry : angle 0.90364 / 0.38 (22793) hydrogen bonds : bond 0.05181 / 3.32 ( 762) hydrogen bonds : angle 4.41902 / 3.29 ( 2211) Misc. bond : bond 0.14287 / 10.71 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4402 (OUTLIER) cc_final: 0.2319 (mmm160) REVERT: B 18 ASN cc_start: 0.5170 (OUTLIER) cc_final: 0.3001 (p0) REVERT: B 25 ASP cc_start: 0.7824 (t0) cc_final: 0.7106 (m-30) REVERT: C 30 THR cc_start: 0.7723 (t) cc_final: 0.7466 (t) REVERT: C 37 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7925 (mm) REVERT: C 144 GLU cc_start: 0.8132 (tt0) cc_final: 0.7781 (tt0) REVERT: C 216 MET cc_start: 0.8712 (mpp) cc_final: 0.7907 (mmt) REVERT: D 13 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 23 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8707 (mt) REVERT: E 47 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7411 (mm) REVERT: G 25 ASP cc_start: 0.6832 (t0) cc_final: 0.6585 (t0) REVERT: G 31 PHE cc_start: 0.8712 (t80) cc_final: 0.8481 (t80) REVERT: G 49 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7947 (ttpt) REVERT: I 29 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7093 (tttm) REVERT: K 7 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5917 (mm) REVERT: L 77 ILE cc_start: 0.8234 (mt) cc_final: 0.7802 (tt) REVERT: L 87 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (mm-30) REVERT: M 186 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8424 (t80) REVERT: M 205 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7832 (tt) REVERT: M 218 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.5845 (mptt) REVERT: Q 17 LEU cc_start: 0.7828 (tp) cc_final: 0.7525 (tp) outliers start: 66 outliers final: 41 residues processed: 262 average time/residue: 0.1174 time to fit residues: 47.6386 Evaluate side-chains 259 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 186 PHE Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 24 HIS Chi-restraints excluded: chain P residue 25 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 ASN M 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126330 restraints weight = 25405.790| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.76 r_work: 0.3429 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.465 16382 Z= 0.166 Angle : 0.818 17.934 22793 Z= 0.345 Chirality : 0.042 0.156 2206 Planarity : 0.005 0.075 2858 Dihedral : 17.902 179.604 2819 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.33 % Favored : 93.36 % Rotamer: Outliers : 4.53 % Allowed : 20.30 % Favored : 75.18 % 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: 0.54 (0.21), residues: 1626 helix: 1.77 (0.16), residues: 942 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 91 TYR 0.015 0.001 TYR C 320 PHE 0.026 0.002 PHE Q 14 TRP 0.016 0.001 TRP B 48 HIS 0.005 0.001 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (16350) covalent geometry : angle 0.81801 / 0.34 (22793) hydrogen bonds : bond 0.04642 / 2.96 ( 762) hydrogen bonds : angle 4.30529 / 3.21 ( 2211) Misc. bond : bond 0.12774 / 9.79 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4226 (OUTLIER) cc_final: 0.2305 (mmt180) REVERT: B 25 ASP cc_start: 0.7621 (t0) cc_final: 0.7093 (m-30) REVERT: C 30 THR cc_start: 0.7715 (t) cc_final: 0.7456 (t) REVERT: C 36 ASP cc_start: 0.7941 (t0) cc_final: 0.7543 (m-30) REVERT: C 144 GLU cc_start: 0.7927 (tt0) cc_final: 0.7654 (tt0) REVERT: C 191 GLU cc_start: 0.8450 (tp30) cc_final: 0.8011 (tp30) REVERT: C 216 MET cc_start: 0.8694 (mpp) cc_final: 0.7969 (mmt) REVERT: D 13 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8312 (mp) REVERT: D 23 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8698 (mp) REVERT: G 25 ASP cc_start: 0.6734 (t0) cc_final: 0.6432 (t0) REVERT: G 31 PHE cc_start: 0.8682 (t80) cc_final: 0.8458 (t80) REVERT: G 49 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7950 (ttpt) REVERT: I 29 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7197 (tttm) REVERT: L 77 ILE cc_start: 0.8213 (mt) cc_final: 0.7834 (tt) REVERT: M 12 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7222 (pt0) REVERT: M 186 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8331 (t80) REVERT: M 204 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8475 (tp) REVERT: M 205 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7778 (tt) REVERT: M 218 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.6208 (mptt) REVERT: M 262 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.7874 (t80) REVERT: Q 17 LEU cc_start: 0.7867 (tp) cc_final: 0.7621 (tp) outliers start: 64 outliers final: 40 residues processed: 261 average time/residue: 0.1182 time to fit residues: 47.8748 Evaluate side-chains 251 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 284 CYS Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 12 GLU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 186 PHE Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 11 optimal weight: 0.0470 chunk 59 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123896 restraints weight = 25747.585| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.69 r_work: 0.3383 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.447 16382 Z= 0.138 Angle : 0.777 16.756 22793 Z= 0.330 Chirality : 0.041 0.137 2206 Planarity : 0.005 0.071 2858 Dihedral : 17.549 179.640 2819 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 4.46 % Allowed : 20.58 % Favored : 74.96 % 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: 0.73 (0.21), residues: 1626 helix: 1.92 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 91 TYR 0.012 0.001 TYR L 258 PHE 0.025 0.001 PHE Q 14 TRP 0.016 0.001 TRP B 48 HIS 0.005 0.001 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (16350) covalent geometry : angle 0.77730 / 0.33 (22793) hydrogen bonds : bond 0.04314 / 2.77 ( 762) hydrogen bonds : angle 4.20009 / 3.12 ( 2211) Misc. bond : bond 0.11908 / 9.06 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.2436 (mmt180) REVERT: B 25 ASP cc_start: 0.7495 (t0) cc_final: 0.6965 (m-30) REVERT: C 30 THR cc_start: 0.7682 (t) cc_final: 0.7412 (t) REVERT: C 36 ASP cc_start: 0.7942 (t0) cc_final: 0.7491 (m-30) REVERT: C 86 GLU cc_start: 0.7445 (pt0) cc_final: 0.7180 (mt-10) REVERT: C 144 GLU cc_start: 0.8034 (tt0) cc_final: 0.7666 (tt0) REVERT: C 198 ILE cc_start: 0.8820 (pt) cc_final: 0.8529 (pt) REVERT: C 216 MET cc_start: 0.8698 (mpp) cc_final: 0.7927 (mmt) REVERT: D 13 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8281 (mp) REVERT: D 31 SER cc_start: 0.9062 (m) cc_final: 0.8852 (t) REVERT: E 47 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7230 (mm) REVERT: G 25 ASP cc_start: 0.6736 (t0) cc_final: 0.6432 (t0) REVERT: G 31 PHE cc_start: 0.8697 (t80) cc_final: 0.8449 (t80) REVERT: G 49 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7920 (ttpt) REVERT: I 29 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7166 (tttm) REVERT: J 38 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8557 (mp) REVERT: L 77 ILE cc_start: 0.8143 (mt) cc_final: 0.7841 (tt) REVERT: M 12 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: M 186 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8220 (t80) REVERT: M 205 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7705 (tt) REVERT: M 262 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7901 (t80) REVERT: P 25 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6428 (t0) REVERT: Q 17 LEU cc_start: 0.7790 (tp) cc_final: 0.7542 (tp) outliers start: 63 outliers final: 38 residues processed: 259 average time/residue: 0.1156 time to fit residues: 46.9149 Evaluate side-chains 258 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 12 GLU Chi-restraints excluded: chain M residue 66 PHE Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 186 PHE Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 ASN L 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121919 restraints weight = 26118.851| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.68 r_work: 0.3354 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.455 16382 Z= 0.173 Angle : 0.822 17.237 22793 Z= 0.347 Chirality : 0.043 0.145 2206 Planarity : 0.005 0.067 2858 Dihedral : 17.514 179.606 2819 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.42 % Rotamer: Outliers : 3.96 % Allowed : 21.29 % Favored : 74.75 % 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: 0.73 (0.21), residues: 1626 helix: 1.90 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 91 TYR 0.031 0.002 TYR L 258 PHE 0.026 0.002 PHE Q 14 TRP 0.015 0.001 TRP B 48 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (16350) covalent geometry : angle 0.82159 / 0.35 (22793) hydrogen bonds : bond 0.04546 / 2.92 ( 762) hydrogen bonds : angle 4.24537 / 3.16 ( 2211) Misc. bond : bond 0.12549 / 9.51 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4556 (OUTLIER) cc_final: 0.2470 (mmt180) REVERT: B 25 ASP cc_start: 0.7543 (t0) cc_final: 0.6987 (m-30) REVERT: C 30 THR cc_start: 0.7670 (t) cc_final: 0.7408 (t) REVERT: C 36 ASP cc_start: 0.7978 (t0) cc_final: 0.7545 (m-30) REVERT: C 86 GLU cc_start: 0.7449 (pt0) cc_final: 0.7164 (mt-10) REVERT: C 144 GLU cc_start: 0.7971 (tt0) cc_final: 0.7583 (tt0) REVERT: C 191 GLU cc_start: 0.8497 (tp30) cc_final: 0.8021 (tp30) REVERT: C 216 MET cc_start: 0.8717 (mpp) cc_final: 0.7972 (mmt) REVERT: C 220 ASP cc_start: 0.7889 (m-30) cc_final: 0.7680 (t70) REVERT: D 13 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8298 (mp) REVERT: E 47 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7230 (mm) REVERT: G 25 ASP cc_start: 0.6827 (t0) cc_final: 0.6511 (t0) REVERT: G 31 PHE cc_start: 0.8719 (t80) cc_final: 0.8488 (t80) REVERT: G 49 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8018 (ttpt) REVERT: I 29 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7253 (tttm) REVERT: J 8 ARG cc_start: 0.7394 (mmm-85) cc_final: 0.5222 (ptt180) REVERT: L 77 ILE cc_start: 0.8231 (mt) cc_final: 0.7898 (tt) REVERT: M 12 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7281 (pt0) REVERT: M 186 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8295 (t80) REVERT: M 218 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.6055 (mptt) REVERT: M 262 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.7905 (t80) REVERT: N 53 LYS cc_start: 0.7457 (mttm) cc_final: 0.7193 (mttp) REVERT: P 5 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.5581 (t0) REVERT: P 25 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6414 (t0) REVERT: Q 17 LEU cc_start: 0.7840 (tp) cc_final: 0.7572 (tp) outliers start: 56 outliers final: 38 residues processed: 256 average time/residue: 0.1179 time to fit residues: 47.0378 Evaluate side-chains 260 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 12 GLU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 186 PHE Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 90 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.142446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124911 restraints weight = 25981.590| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.70 r_work: 0.3394 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.441 16382 Z= 0.130 Angle : 0.761 16.214 22793 Z= 0.323 Chirality : 0.041 0.156 2206 Planarity : 0.005 0.064 2858 Dihedral : 17.253 179.772 2819 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.21 % Favored : 93.48 % Rotamer: Outliers : 3.47 % Allowed : 21.92 % Favored : 74.61 % 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: 0.87 (0.21), residues: 1626 helix: 2.03 (0.16), residues: 941 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 91 TYR 0.038 0.001 TYR L 258 PHE 0.025 0.001 PHE Q 14 TRP 0.014 0.001 TRP R 12 HIS 0.005 0.001 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (16350) covalent geometry : angle 0.76132 / 0.32 (22793) hydrogen bonds : bond 0.04157 / 2.68 ( 762) hydrogen bonds : angle 4.14027 / 3.08 ( 2211) Misc. bond : bond 0.11579 / 8.70 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4439 (OUTLIER) cc_final: 0.2589 (mmt180) REVERT: B 25 ASP cc_start: 0.7479 (t0) cc_final: 0.6932 (m-30) REVERT: C 30 THR cc_start: 0.7615 (t) cc_final: 0.7362 (t) REVERT: C 36 ASP cc_start: 0.7947 (t0) cc_final: 0.7483 (m-30) REVERT: C 144 GLU cc_start: 0.8030 (tt0) cc_final: 0.7593 (tt0) REVERT: C 198 ILE cc_start: 0.8850 (pt) cc_final: 0.8555 (pt) REVERT: C 216 MET cc_start: 0.8734 (mpp) cc_final: 0.8004 (mmt) REVERT: C 220 ASP cc_start: 0.7836 (m-30) cc_final: 0.7630 (t70) REVERT: C 271 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8197 (mpp80) REVERT: D 13 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8278 (mp) REVERT: D 31 SER cc_start: 0.9024 (m) cc_final: 0.8823 (t) REVERT: G 25 ASP cc_start: 0.6809 (t0) cc_final: 0.6506 (t0) REVERT: G 31 PHE cc_start: 0.8720 (t80) cc_final: 0.8453 (t80) REVERT: G 49 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7937 (ttpt) REVERT: I 29 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7171 (tttm) REVERT: J 8 ARG cc_start: 0.7105 (mmm-85) cc_final: 0.5068 (ptt180) REVERT: J 38 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (mp) REVERT: L 52 PHE cc_start: 0.7719 (m-80) cc_final: 0.7469 (m-10) REVERT: L 77 ILE cc_start: 0.8121 (mt) cc_final: 0.7844 (tt) REVERT: M 262 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7971 (t80) REVERT: P 25 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6341 (t0) REVERT: Q 17 LEU cc_start: 0.7792 (tp) cc_final: 0.7538 (tp) outliers start: 49 outliers final: 33 residues processed: 255 average time/residue: 0.1207 time to fit residues: 47.5698 Evaluate side-chains 251 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 8 optimal weight: 8.9990 chunk 141 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 0.0010 chunk 149 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.144419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127095 restraints weight = 25798.478| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.72 r_work: 0.3419 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.418 16382 Z= 0.124 Angle : 0.746 15.283 22793 Z= 0.317 Chirality : 0.040 0.143 2206 Planarity : 0.005 0.061 2858 Dihedral : 16.907 179.788 2819 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.09 % Favored : 93.67 % Rotamer: Outliers : 2.55 % Allowed : 23.06 % Favored : 74.40 % 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: 1.01 (0.21), residues: 1626 helix: 2.12 (0.16), residues: 941 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 91 TYR 0.037 0.001 TYR L 258 PHE 0.027 0.001 PHE K 16 TRP 0.014 0.001 TRP R 12 HIS 0.004 0.001 HIS L 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (16350) covalent geometry : angle 0.74619 / 0.32 (22793) hydrogen bonds : bond 0.03943 / 2.54 ( 762) hydrogen bonds : angle 4.06833 / 3.02 ( 2211) Misc. bond : bond 0.11027 / 8.10 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.4252 (OUTLIER) cc_final: 0.2636 (mmt180) REVERT: B 25 ASP cc_start: 0.7314 (t0) cc_final: 0.6781 (m-30) REVERT: C 30 THR cc_start: 0.7633 (t) cc_final: 0.7394 (t) REVERT: C 36 ASP cc_start: 0.7879 (t0) cc_final: 0.7423 (m-30) REVERT: C 119 MET cc_start: 0.9028 (ttm) cc_final: 0.8760 (mtm) REVERT: C 144 GLU cc_start: 0.7956 (tt0) cc_final: 0.7523 (tt0) REVERT: C 191 GLU cc_start: 0.8438 (tp30) cc_final: 0.7997 (tp30) REVERT: C 198 ILE cc_start: 0.8858 (pt) cc_final: 0.8560 (pt) REVERT: C 216 MET cc_start: 0.8677 (mpp) cc_final: 0.7973 (mmt) REVERT: C 271 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8256 (mpp80) REVERT: D 13 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 31 SER cc_start: 0.8863 (m) cc_final: 0.8612 (t) REVERT: G 25 ASP cc_start: 0.6799 (t0) cc_final: 0.6506 (t0) REVERT: G 49 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7920 (ttpt) REVERT: J 8 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.5009 (ptt180) REVERT: L 52 PHE cc_start: 0.7649 (m-80) cc_final: 0.7412 (m-10) REVERT: L 77 ILE cc_start: 0.8116 (mt) cc_final: 0.7872 (tt) REVERT: L 96 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7264 (mm) REVERT: M 218 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.6132 (mptt) REVERT: M 262 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.7965 (t80) REVERT: P 25 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6344 (t0) REVERT: Q 17 LEU cc_start: 0.7680 (tp) cc_final: 0.7430 (tp) outliers start: 36 outliers final: 27 residues processed: 237 average time/residue: 0.1157 time to fit residues: 43.1581 Evaluate side-chains 234 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 193 HIS Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129778 restraints weight = 25525.530| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.70 r_work: 0.3478 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.423 16382 Z= 0.138 Angle : 0.768 15.565 22793 Z= 0.323 Chirality : 0.041 0.162 2206 Planarity : 0.005 0.058 2858 Dihedral : 16.699 179.734 2817 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.36 % Rotamer: Outliers : 2.90 % Allowed : 22.49 % Favored : 74.61 % 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: 1.03 (0.21), residues: 1626 helix: 2.12 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 91 TYR 0.038 0.001 TYR L 258 PHE 0.046 0.002 PHE I 34 TRP 0.015 0.001 TRP B 48 HIS 0.004 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (16350) covalent geometry : angle 0.76795 / 0.32 (22793) hydrogen bonds : bond 0.04116 / 2.66 ( 762) hydrogen bonds : angle 4.07522 / 3.02 ( 2211) Misc. bond : bond 0.11723 / 8.69 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.22 seconds wall clock time: 72 minutes 40.49 seconds (4360.49 seconds total)