Starting phenix.real_space_refine on Sun Jul 5 17:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kk2_62382/07_2026/9kk2_62382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kk2_62382/07_2026/9kk2_62382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kk2_62382/07_2026/9kk2_62382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kk2_62382/07_2026/9kk2_62382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kk2_62382/07_2026/9kk2_62382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kk2_62382/07_2026/9kk2_62382.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 171 5.49 5 Mg 2 5.21 5 S 91 5.16 5 C 17642 2.51 5 N 5073 2.21 5 O 5889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28870 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2473 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain: "B" Number of atoms: 4256 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 528, 4234 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 528, 4234 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain breaks: 2 bond proxies already assigned to first conformer: 4281 Chain: "C" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4283 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 Chain: "D" Number of atoms: 4307 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 536, 4289 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 15, 'TRANS': 520} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 536, 4289 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 15, 'TRANS': 520} Chain breaks: 1 bond proxies already assigned to first conformer: 4340 Chain: "E" Number of atoms: 4149 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4142 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 15, 'TRANS': 500} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 516, 4142 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 15, 'TRANS': 500} Chain breaks: 4 bond proxies already assigned to first conformer: 4201 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "G" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 869 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna2p': 14, 'rna3p': 26} Chain: "I" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1501 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "K" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2473 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 869 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna2p': 14, 'rna3p': 26} Chain: "M" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19821 SG CYS F 43 64.586 88.393 157.481 1.00 63.54 S ATOM 19844 SG CYS F 46 63.190 90.071 154.489 1.00 63.74 S ATOM 20115 SG CYS F 78 64.282 86.565 153.977 1.00 66.79 S ATOM 20204 SG CYS F 90 66.649 89.535 154.259 1.00 64.27 S ATOM 21522 SG CYS G 43 62.990 43.502 31.408 1.00 67.88 S ATOM 21545 SG CYS G 46 61.811 42.485 34.762 1.00 65.47 S ATOM 21816 SG CYS G 78 62.822 46.036 34.504 1.00 68.76 S ATOM 21905 SG CYS G 90 65.250 43.105 34.711 1.00 69.35 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 67 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 67 " occ=0.50 residue: pdb=" N AARG B 221 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 221 " occ=0.50 residue: pdb=" N AARG D 76 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 76 " occ=0.50 Time building chain proxies: 7.76, per 1000 atoms: 0.27 Number of scatterers: 28870 At special positions: 0 Unit cell: (129.48, 140.436, 188.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 91 16.00 P 171 15.00 Mg 2 11.99 O 5889 8.00 N 5073 7.00 C 17642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 46 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 78 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " Number of angles added : 12 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5954 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 26 sheets defined 55.3% alpha, 12.1% beta 55 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.314A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.837A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 250 through 266 Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.787A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.917A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 256 through 277 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 309 through 326 removed outlier: 3.514A pdb=" N VAL B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 379 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 434 through 435 No H-bonds generated for 'chain 'B' and resid 434 through 435' Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 465 through 473 Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 487 through 499 Processing helix chain 'B' and resid 504 through 519 Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 98 through 119 removed outlier: 3.964A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.627A pdb=" N GLU C 223 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 226 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 255 Processing helix chain 'C' and resid 256 through 277 removed outlier: 3.521A pdb=" N SER C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 282 through 306 Processing helix chain 'C' and resid 310 through 326 Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 358 through 379 Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 434 through 435 No H-bonds generated for 'chain 'C' and resid 434 through 435' Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 465 through 473 Processing helix chain 'C' and resid 483 through 486 Processing helix chain 'C' and resid 487 through 499 Processing helix chain 'C' and resid 504 through 519 Processing helix chain 'C' and resid 522 through 547 Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 95 through 119 removed outlier: 3.664A pdb=" N LYS D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 238 through 255 Processing helix chain 'D' and resid 258 through 277 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 282 through 306 Processing helix chain 'D' and resid 310 through 326 Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 379 Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'D' and resid 434 through 435 No H-bonds generated for 'chain 'D' and resid 434 through 435' Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 465 through 473 Processing helix chain 'D' and resid 483 through 486 Processing helix chain 'D' and resid 487 through 499 Processing helix chain 'D' and resid 504 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 37 through 49 Processing helix chain 'E' and resid 98 through 119 removed outlier: 3.888A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 238 through 254 Processing helix chain 'E' and resid 260 through 275 Processing helix chain 'E' and resid 282 through 302 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 326 Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 358 through 379 Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 408 through 417 removed outlier: 3.720A pdb=" N ASN E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 413 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 434 through 435 No H-bonds generated for 'chain 'E' and resid 434 through 435' Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 465 through 473 Processing helix chain 'E' and resid 483 through 486 Processing helix chain 'E' and resid 487 through 499 Processing helix chain 'E' and resid 504 through 519 Processing helix chain 'E' and resid 522 through 544 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.528A pdb=" N LEU F 13 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 40 removed outlier: 4.047A pdb=" N VAL F 31 " --> pdb=" O ASP F 27 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 113 through 116 removed outlier: 3.614A pdb=" N ASP F 116 " --> pdb=" O ASN F 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 116' Processing helix chain 'F' and resid 134 through 148 Processing helix chain 'F' and resid 152 through 176 removed outlier: 3.810A pdb=" N ILE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.674A pdb=" N GLU F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 201 through 210 removed outlier: 3.522A pdb=" N ALA F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 15 removed outlier: 3.532A pdb=" N LEU G 13 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 40 removed outlier: 4.045A pdb=" N VAL G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 113 through 116 removed outlier: 3.620A pdb=" N ASP G 116 " --> pdb=" O ASN G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 116' Processing helix chain 'G' and resid 134 through 148 Processing helix chain 'G' and resid 152 through 176 removed outlier: 3.830A pdb=" N ILE G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 3.501A pdb=" N LEU G 176 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.689A pdb=" N GLU G 187 " --> pdb=" O ASP G 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET G 188 " --> pdb=" O ASP G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 201 through 210 removed outlier: 3.533A pdb=" N ALA G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 12 Processing helix chain 'K' and resid 14 through 23 Processing helix chain 'K' and resid 24 through 27 Processing helix chain 'K' and resid 48 through 62 Processing helix chain 'K' and resid 78 through 85 Processing helix chain 'K' and resid 100 through 104 Processing helix chain 'K' and resid 105 through 116 Processing helix chain 'K' and resid 124 through 136 removed outlier: 4.335A pdb=" N LEU K 129 " --> pdb=" O PRO K 125 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE K 130 " --> pdb=" O GLN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 164 Processing helix chain 'K' and resid 164 through 178 removed outlier: 3.830A pdb=" N VAL K 178 " --> pdb=" O ALA K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 200 Processing helix chain 'K' and resid 201 through 215 Processing helix chain 'K' and resid 221 through 225 Processing helix chain 'K' and resid 250 through 266 Processing helix chain 'K' and resid 270 through 288 Processing helix chain 'K' and resid 288 through 300 removed outlier: 3.751A pdb=" N ILE K 292 " --> pdb=" O GLU K 288 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER K 300 " --> pdb=" O ASN K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 185 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 236 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 83 removed outlier: 6.466A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE B 74 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N TYR B 141 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.810A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL B 90 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 335 removed outlier: 3.905A pdb=" N ASN B 331 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 83 removed outlier: 6.426A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU C 66 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 149 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE C 74 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N TYR C 141 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE C 150 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS C 155 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.760A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 89 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 90 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 329 through 337 removed outlier: 3.881A pdb=" N ASN C 331 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.511A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU D 66 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE D 149 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE D 74 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N TYR D 141 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE D 150 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS D 155 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.776A pdb=" N GLY D 390 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE D 423 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 90 " --> pdb=" O ARG D 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 329 through 337 removed outlier: 3.871A pdb=" N ASN D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 50 through 52 Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 83 removed outlier: 6.509A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU E 66 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE E 149 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N TYR E 141 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE E 150 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS E 155 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 199 through 203 removed outlier: 6.724A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 90 " --> pdb=" O ARG E 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 329 through 335 removed outlier: 3.899A pdb=" N ASN E 331 " --> pdb=" O THR E 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AC3, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AC4, first strand: chain 'G' and resid 53 through 57 Processing sheet with id=AC5, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AC6, first strand: chain 'K' and resid 29 through 35 Processing sheet with id=AC7, first strand: chain 'K' and resid 181 through 185 Processing sheet with id=AC8, first strand: chain 'K' and resid 234 through 236 removed outlier: 4.523A pdb=" N ARG K 234 " --> pdb=" O ILE K 241 " (cutoff:3.500A) 1345 hydrogen bonds defined for protein. 3814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4816 1.32 - 1.45: 8472 1.45 - 1.57: 15935 1.57 - 1.69: 381 1.69 - 1.81: 152 Bond restraints: 29756 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C5 ADP B 601 " pdb=" C6 ADP B 601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" CA SER D 522 " pdb=" CB SER D 522 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.58e-02 4.01e+03 1.62e+01 ... (remaining 29751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 37480 2.93 - 5.86: 2900 5.86 - 8.79: 489 8.79 - 11.72: 62 11.72 - 14.65: 7 Bond angle restraints: 40938 Sorted by residual: angle pdb=" CA PHE B 453 " pdb=" CB PHE B 453 " pdb=" CG PHE B 453 " ideal model delta sigma weight residual 113.80 124.18 -10.38 1.00e+00 1.00e+00 1.08e+02 angle pdb=" O3' A H 42 " pdb=" P A H 43 " pdb=" O5' A H 43 " ideal model delta sigma weight residual 104.00 89.35 14.65 1.50e+00 4.44e-01 9.54e+01 angle pdb=" CA PHE E 453 " pdb=" CB PHE E 453 " pdb=" CG PHE E 453 " ideal model delta sigma weight residual 113.80 123.31 -9.51 1.00e+00 1.00e+00 9.05e+01 angle pdb=" N VAL G 126 " pdb=" CA VAL G 126 " pdb=" CB VAL G 126 " ideal model delta sigma weight residual 110.72 121.06 -10.34 1.09e+00 8.42e-01 9.00e+01 angle pdb=" O3' U H 45 " pdb=" P U H 46 " pdb=" O5' U H 46 " ideal model delta sigma weight residual 104.00 89.98 14.02 1.50e+00 4.44e-01 8.74e+01 ... (remaining 40933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 17034 35.27 - 70.54: 789 70.54 - 105.82: 90 105.82 - 141.09: 1 141.09 - 176.36: 1 Dihedral angle restraints: 17915 sinusoidal: 8732 harmonic: 9183 Sorted by residual: dihedral pdb=" CA ASP C 217 " pdb=" C ASP C 217 " pdb=" N ASN C 218 " pdb=" CA ASN C 218 " ideal model delta harmonic sigma weight residual -180.00 -146.43 -33.57 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" C ASP K 17 " pdb=" N ASP K 17 " pdb=" CA ASP K 17 " pdb=" CB ASP K 17 " ideal model delta harmonic sigma weight residual -122.60 -138.81 16.21 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" C ASP A 17 " pdb=" N ASP A 17 " pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " ideal model delta harmonic sigma weight residual -122.60 -138.66 16.06 0 2.50e+00 1.60e-01 4.12e+01 ... (remaining 17912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4007 0.133 - 0.266: 574 0.266 - 0.400: 28 0.400 - 0.533: 1 0.533 - 0.666: 6 Chirality restraints: 4616 Sorted by residual: chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P DT M 68 " pdb=" OP1 DT M 68 " pdb=" OP2 DT M 68 " pdb=" O5' DT M 68 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASP A 17 " pdb=" N ASP A 17 " pdb=" C ASP A 17 " pdb=" CB ASP A 17 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 4613 not shown) Planarity restraints: 4684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G H 23 " -0.092 2.00e-02 2.50e+03 3.77e-02 4.26e+01 pdb=" N9 G H 23 " 0.072 2.00e-02 2.50e+03 pdb=" C8 G H 23 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G H 23 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G H 23 " 0.012 2.00e-02 2.50e+03 pdb=" C6 G H 23 " -0.023 2.00e-02 2.50e+03 pdb=" O6 G H 23 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G H 23 " -0.022 2.00e-02 2.50e+03 pdb=" C2 G H 23 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G H 23 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G H 23 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G H 23 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 245 " 0.068 2.00e-02 2.50e+03 3.58e-02 3.20e+01 pdb=" CG TRP B 245 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 245 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 245 " -0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP B 245 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 245 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 245 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 245 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 245 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 245 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 163 " 0.319 9.50e-02 1.11e+02 1.48e-01 3.12e+01 pdb=" NE ARG D 163 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 163 " -0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG D 163 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG D 163 " 0.035 2.00e-02 2.50e+03 ... (remaining 4681 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 560 2.68 - 3.24: 25678 3.24 - 3.79: 48180 3.79 - 4.35: 65348 4.35 - 4.90: 102107 Nonbonded interactions: 241873 Sorted by model distance: nonbonded pdb=" OP2 U H 49 " pdb="MG MG H 200 " model vdw 2.130 2.170 nonbonded pdb=" OG1 THR E 194 " pdb=" O VAL E 304 " model vdw 2.165 3.040 nonbonded pdb=" O PHE E 200 " pdb=" OG1 THR E 232 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP C 184 " pdb=" NH1 ARG C 187 " model vdw 2.236 3.120 nonbonded pdb=" O ASP C 301 " pdb=" OG SER C 305 " model vdw 2.267 3.040 ... (remaining 241868 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' selection = chain 'K' } ncs_group { reference = (chain 'B' and (resid 2 through 24 or resid 37 through 66 or resid 68 through 75 \ or resid 77 through 210 or resid 222 through 240 or resid 242 through 255 or re \ sid 259 through 275 or resid 280 through 401 or resid 403 through 545)) selection = (chain 'C' and (resid 2 through 24 or resid 37 through 66 or resid 68 through 75 \ or resid 77 through 210 or resid 222 through 240 or resid 242 through 255 or re \ sid 259 through 275 or resid 280 through 302 or resid 308 through 401 or resid 4 \ 03 through 545)) selection = (chain 'D' and (resid 2 through 24 or resid 37 through 66 or resid 68 through 75 \ or resid 77 through 210 or resid 222 through 240 or resid 242 through 255 or re \ sid 259 through 275 or resid 280 through 302 or resid 308 through 401 or resid 4 \ 03 through 545)) selection = (chain 'E' and (resid 2 through 24 or resid 37 through 66 or resid 68 through 75 \ or resid 77 through 210 or resid 222 through 240 or resid 242 through 302 or re \ sid 308 through 401 or resid 403 through 545)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'L' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 32.110 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.011 0.114 29764 Z= 0.654 Angle : 1.800 14.653 40950 Z= 1.149 Chirality : 0.092 0.666 4616 Planarity : 0.008 0.148 4684 Dihedral : 18.361 176.360 11961 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.33 % Allowed : 5.58 % Favored : 91.09 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.66 (0.14), residues: 3130 helix: 0.93 (0.12), residues: 1505 sheet: 0.33 (0.25), residues: 409 loop : 0.02 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.005 ARG D 163 TYR 0.036 0.006 TYR D 141 PHE 0.033 0.006 PHE B 242 TRP 0.068 0.009 TRP B 245 HIS 0.019 0.003 HIS E 400 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.65 (29756) covalent geometry : angle 1.79568 / 1.15 (40938) hydrogen bonds : bond 0.17837 / 11.84 ( 1484) hydrogen bonds : angle 6.01549 / 4.34 ( 4064) metal coordination : bond 0.00876 / 0.54 ( 8) metal coordination : angle 7.28868 / 3.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 542 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6739 (mtp85) REVERT: A 60 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7124 (mm-40) REVERT: A 68 ASP cc_start: 0.7642 (m-30) cc_final: 0.7438 (m-30) REVERT: A 74 MET cc_start: 0.8290 (mmm) cc_final: 0.7953 (mmm) REVERT: A 75 LYS cc_start: 0.8304 (tppp) cc_final: 0.8087 (mmtt) REVERT: A 122 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 171 ILE cc_start: 0.7867 (tp) cc_final: 0.7558 (tp) REVERT: A 177 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8115 (mtmm) REVERT: A 188 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7739 (t70) REVERT: A 211 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7158 (ttmm) REVERT: A 224 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8419 (mmmm) REVERT: A 245 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7041 (mm-30) REVERT: B 10 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8514 (mttm) REVERT: B 23 ARG cc_start: 0.7459 (mmp80) cc_final: 0.7042 (mtp85) REVERT: B 83 LYS cc_start: 0.8918 (tmtm) cc_final: 0.8333 (ttpp) REVERT: B 119 LYS cc_start: 0.8658 (mttt) cc_final: 0.8032 (mptt) REVERT: B 170 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7428 (mp0) REVERT: B 271 LEU cc_start: 0.3683 (OUTLIER) cc_final: 0.3306 (mm) REVERT: B 320 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7260 (mmtm) REVERT: B 414 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7801 (mmm160) REVERT: B 448 ASP cc_start: 0.7484 (t70) cc_final: 0.7254 (t0) REVERT: B 462 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8372 (ttpt) REVERT: B 466 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7270 (m110) REVERT: B 533 ARG cc_start: 0.7118 (ttp-110) cc_final: 0.6845 (ttp-110) REVERT: B 536 LYS cc_start: 0.7085 (ttpp) cc_final: 0.6522 (pttt) REVERT: B 537 MET cc_start: 0.7077 (mmt) cc_final: 0.6759 (mtt) REVERT: C 68 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7723 (ttm170) REVERT: C 136 ASP cc_start: 0.7452 (p0) cc_final: 0.7127 (p0) REVERT: C 140 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6705 (mmm160) REVERT: C 152 LYS cc_start: 0.7896 (mttt) cc_final: 0.7524 (mppt) REVERT: C 155 LYS cc_start: 0.8115 (mttt) cc_final: 0.7769 (mttm) REVERT: C 216 LYS cc_start: 0.7678 (mmtt) cc_final: 0.6707 (mmmm) REVERT: C 272 GLN cc_start: 0.4786 (OUTLIER) cc_final: 0.4126 (mp10) REVERT: C 274 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3329 (p) REVERT: C 279 MET cc_start: -0.0137 (mmp) cc_final: -0.0380 (ttt) REVERT: C 316 SER cc_start: 0.8092 (t) cc_final: 0.7770 (p) REVERT: C 318 VAL cc_start: 0.8140 (t) cc_final: 0.7856 (m) REVERT: C 342 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8019 (tt) REVERT: C 383 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7378 (mp0) REVERT: C 396 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7552 (tt0) REVERT: C 436 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7400 (mt-10) REVERT: C 465 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7599 (tm-30) REVERT: D 41 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: D 67 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8290 (mtm180) REVERT: D 95 ASN cc_start: 0.8010 (t0) cc_final: 0.7655 (t0) REVERT: D 97 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7443 (tttm) REVERT: D 119 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7610 (mmtm) REVERT: D 125 GLN cc_start: 0.8753 (mt0) cc_final: 0.8419 (mt0) REVERT: D 140 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7918 (mtm110) REVERT: D 152 LYS cc_start: 0.8338 (mttt) cc_final: 0.8093 (mmtm) REVERT: D 212 ASN cc_start: 0.6456 (m-40) cc_final: 0.6091 (t0) REVERT: D 221 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.7077 (mtp85) REVERT: D 224 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6944 (tm-30) REVERT: D 279 MET cc_start: -0.0753 (mtt) cc_final: -0.1026 (tpt) REVERT: D 293 LEU cc_start: 0.2609 (OUTLIER) cc_final: 0.2342 (tt) REVERT: D 336 MET cc_start: 0.7027 (mmt) cc_final: 0.6784 (mmm) REVERT: D 359 ASP cc_start: 0.8110 (m-30) cc_final: 0.7670 (m-30) REVERT: D 383 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7707 (mm-30) REVERT: D 444 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6063 (tp30) REVERT: D 466 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7100 (t0) REVERT: D 474 MET cc_start: 0.8694 (mtp) cc_final: 0.8411 (mtp) REVERT: D 505 ASN cc_start: 0.7095 (t0) cc_final: 0.6415 (p0) REVERT: D 535 ASN cc_start: 0.7656 (m-40) cc_final: 0.7354 (m-40) REVERT: E 41 GLU cc_start: 0.6871 (tp30) cc_final: 0.6524 (mp0) REVERT: E 83 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8192 (ttpp) REVERT: E 138 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7537 (mp0) REVERT: E 152 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8229 (mptm) REVERT: E 206 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7638 (mp0) REVERT: E 244 GLU cc_start: 0.8226 (tt0) cc_final: 0.7812 (tm-30) REVERT: E 320 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7453 (ttpt) REVERT: E 444 GLU cc_start: 0.5785 (mt-10) cc_final: 0.5561 (tm-30) REVERT: E 450 ASP cc_start: 0.7435 (m-30) cc_final: 0.6500 (p0) REVERT: E 466 ASN cc_start: 0.7690 (t0) cc_final: 0.7458 (m-40) REVERT: E 526 LYS cc_start: 0.6879 (mttm) cc_final: 0.6666 (mtpt) REVERT: E 535 ASN cc_start: 0.8411 (m-40) cc_final: 0.8185 (m-40) REVERT: F 3 GLU cc_start: 0.7504 (tt0) cc_final: 0.7119 (tp30) REVERT: F 8 GLU cc_start: 0.6958 (tp30) cc_final: 0.6548 (pt0) REVERT: F 11 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6597 (pp20) REVERT: F 14 ASP cc_start: 0.7689 (m-30) cc_final: 0.7438 (m-30) REVERT: F 17 ILE cc_start: 0.7261 (mm) cc_final: 0.7055 (tp) REVERT: F 37 GLU cc_start: 0.7523 (tt0) cc_final: 0.7101 (tp30) REVERT: F 80 ASP cc_start: 0.8183 (t70) cc_final: 0.7736 (t0) REVERT: F 82 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6477 (mmt90) REVERT: F 83 LYS cc_start: 0.7462 (mttm) cc_final: 0.6874 (mtmt) REVERT: F 107 ILE cc_start: 0.8565 (mt) cc_final: 0.8225 (mp) REVERT: F 108 LYS cc_start: 0.8129 (tttt) cc_final: 0.7507 (tttp) REVERT: F 125 GLU cc_start: 0.8125 (tt0) cc_final: 0.7829 (tt0) REVERT: F 167 MET cc_start: 0.8694 (mmm) cc_final: 0.8389 (mmm) REVERT: F 182 GLU cc_start: 0.6805 (mm-30) cc_final: 0.5913 (tt0) REVERT: F 184 ASP cc_start: 0.7320 (m-30) cc_final: 0.6925 (t0) REVERT: G 52 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6940 (mtt180) REVERT: G 72 ASN cc_start: 0.7205 (m-40) cc_final: 0.6741 (m-40) REVERT: G 82 ARG cc_start: 0.5523 (mtm-85) cc_final: 0.5232 (mmt90) REVERT: G 105 ASP cc_start: 0.7188 (m-30) cc_final: 0.6839 (m-30) REVERT: G 167 MET cc_start: 0.8531 (mmm) cc_final: 0.8328 (mmm) REVERT: G 186 ASN cc_start: 0.7391 (m-40) cc_final: 0.6939 (m-40) REVERT: G 190 ARG cc_start: 0.6518 (ttp-110) cc_final: 0.6204 (mtm110) REVERT: K 71 MET cc_start: 0.7067 (mmm) cc_final: 0.6696 (mmm) REVERT: K 81 ASP cc_start: 0.6213 (m-30) cc_final: 0.5959 (m-30) REVERT: K 115 MET cc_start: 0.5721 (tpp) cc_final: 0.5466 (mtt) REVERT: K 179 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6070 (tm-30) REVERT: K 207 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7000 (mt-10) REVERT: K 226 VAL cc_start: 0.7484 (t) cc_final: 0.7283 (p) REVERT: K 245 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6046 (mm-30) REVERT: K 270 ASP cc_start: 0.4551 (p0) cc_final: 0.4200 (p0) REVERT: K 299 TYR cc_start: 0.5493 (m-80) cc_final: 0.5099 (m-80) outliers start: 92 outliers final: 13 residues processed: 603 average time/residue: 0.7542 time to fit residues: 520.5367 Evaluate side-chains 412 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 403 PRO Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain K residue 120 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 221 ASN B 22 GLN B 460 GLN B 468 GLN C 94 ASN C 460 GLN D 13 ASN D 508 GLN E 13 ASN E 95 ASN E 116 ASN E 460 GLN E 513 GLN F 28 GLN F 51 ASN F 113 ASN F 164 GLN G 28 GLN K 102 ASN K 221 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120181 restraints weight = 49224.145| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.39 r_work: 0.2911 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29764 Z= 0.164 Angle : 0.641 7.693 40950 Z= 0.349 Chirality : 0.044 0.213 4616 Planarity : 0.004 0.064 4684 Dihedral : 17.412 176.667 5710 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.22 % Favored : 98.72 % Rotamer: Outliers : 3.01 % Allowed : 11.78 % Favored : 85.22 % 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: 1.46 (0.15), residues: 3130 helix: 1.89 (0.13), residues: 1542 sheet: 0.20 (0.24), residues: 463 loop : 0.10 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 362 TYR 0.028 0.002 TYR C 141 PHE 0.018 0.002 PHE B 113 TRP 0.019 0.002 TRP D 245 HIS 0.008 0.001 HIS E 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (29756) covalent geometry : angle 0.63938 / 0.35 (40938) hydrogen bonds : bond 0.05683 / 3.80 ( 1484) hydrogen bonds : angle 4.48597 / 3.25 ( 4064) metal coordination : bond 0.00439 / 0.25 ( 8) metal coordination : angle 3.07577 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 382 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6847 (mtm110) REVERT: A 60 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7525 (mm-40) REVERT: A 122 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: A 176 LYS cc_start: 0.8662 (tttm) cc_final: 0.8392 (tttp) REVERT: A 177 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8351 (mtmm) REVERT: A 211 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7969 (ttmm) REVERT: A 219 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7686 (mtp-110) REVERT: A 245 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7748 (mm-30) REVERT: B 119 LYS cc_start: 0.8650 (mttt) cc_final: 0.8380 (mtmp) REVERT: B 170 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7652 (tm-30) REVERT: B 320 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8345 (ttpt) REVERT: B 404 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8373 (ttmt) REVERT: B 414 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8214 (mmm160) REVERT: B 437 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8610 (ttmt) REVERT: B 499 ASN cc_start: 0.7332 (t0) cc_final: 0.7041 (t0) REVERT: B 533 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7702 (ttp-110) REVERT: B 536 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7004 (pttt) REVERT: B 537 MET cc_start: 0.7699 (mmt) cc_final: 0.7437 (mmm) REVERT: C 68 ARG cc_start: 0.8494 (ttm170) cc_final: 0.8180 (ttm-80) REVERT: C 126 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7936 (mtp180) REVERT: C 136 ASP cc_start: 0.7517 (p0) cc_final: 0.7260 (p0) REVERT: C 152 LYS cc_start: 0.7964 (mttt) cc_final: 0.7722 (mppt) REVERT: C 155 LYS cc_start: 0.8412 (mttt) cc_final: 0.8134 (mttm) REVERT: C 216 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7020 (mtpp) REVERT: C 221 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7303 (mtt180) REVERT: C 318 VAL cc_start: 0.8852 (t) cc_final: 0.8635 (m) REVERT: C 383 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7876 (mp0) REVERT: C 404 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8628 (ttmt) REVERT: C 436 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8051 (mt-10) REVERT: D 41 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: D 279 MET cc_start: -0.0460 (mtt) cc_final: -0.0753 (tpt) REVERT: D 359 ASP cc_start: 0.8333 (m-30) cc_final: 0.7977 (m-30) REVERT: D 444 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6722 (pp20) REVERT: D 450 ASP cc_start: 0.7769 (t0) cc_final: 0.7444 (t0) REVERT: D 466 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7488 (t0) REVERT: D 505 ASN cc_start: 0.7014 (t0) cc_final: 0.6296 (p0) REVERT: D 523 ILE cc_start: 0.8699 (tt) cc_final: 0.8345 (tp) REVERT: D 535 ASN cc_start: 0.8065 (m-40) cc_final: 0.7760 (m-40) REVERT: E 6 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7439 (mt-10) REVERT: E 83 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: E 138 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7852 (mm-30) REVERT: E 143 ASP cc_start: 0.8809 (m-30) cc_final: 0.8530 (m-30) REVERT: E 244 GLU cc_start: 0.8965 (tt0) cc_final: 0.8652 (tm-30) REVERT: E 471 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: E 474 MET cc_start: 0.9023 (mtt) cc_final: 0.8752 (mtt) REVERT: E 537 MET cc_start: 0.7570 (mtm) cc_final: 0.7333 (mtm) REVERT: F 3 GLU cc_start: 0.7773 (tt0) cc_final: 0.7545 (tp30) REVERT: F 8 GLU cc_start: 0.6945 (tp30) cc_final: 0.6606 (pt0) REVERT: F 9 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7272 (ttp80) REVERT: F 37 GLU cc_start: 0.8045 (tt0) cc_final: 0.7614 (mm-30) REVERT: F 82 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6989 (mmt90) REVERT: F 104 ASP cc_start: 0.7009 (m-30) cc_final: 0.6249 (p0) REVERT: F 108 LYS cc_start: 0.8551 (tttt) cc_final: 0.8317 (tttm) REVERT: F 139 LYS cc_start: 0.7659 (ttmp) cc_final: 0.7353 (ttmt) REVERT: F 161 THR cc_start: 0.8757 (m) cc_final: 0.8555 (p) REVERT: F 164 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7926 (mp-120) REVERT: F 167 MET cc_start: 0.8694 (mmm) cc_final: 0.8481 (tpt) REVERT: F 182 GLU cc_start: 0.6718 (mm-30) cc_final: 0.5900 (tt0) REVERT: F 190 ARG cc_start: 0.7696 (mtt-85) cc_final: 0.6679 (mmt180) REVERT: F 195 LYS cc_start: 0.6847 (tptm) cc_final: 0.5507 (ttpp) REVERT: G 52 ARG cc_start: 0.7373 (mtt90) cc_final: 0.6950 (mtm-85) REVERT: G 117 TYR cc_start: 0.8085 (m-80) cc_final: 0.7865 (m-80) REVERT: K 28 LYS cc_start: 0.5774 (mttp) cc_final: 0.5457 (mttt) REVERT: K 71 MET cc_start: 0.7528 (mmm) cc_final: 0.7167 (mmm) REVERT: K 114 GLU cc_start: 0.5588 (tm-30) cc_final: 0.5054 (tm-30) REVERT: K 179 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6565 (tm-30) REVERT: K 224 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7575 (mmtm) REVERT: K 245 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6326 (mm-30) REVERT: K 301 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5968 (tp) outliers start: 83 outliers final: 25 residues processed: 434 average time/residue: 0.7210 time to fit residues: 357.5440 Evaluate side-chains 372 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 84 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 ASN C 499 ASN D 13 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN F 164 GLN G 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117829 restraints weight = 50003.518| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.46 r_work: 0.2897 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29764 Z= 0.153 Angle : 0.580 9.289 40950 Z= 0.314 Chirality : 0.043 0.343 4616 Planarity : 0.004 0.056 4684 Dihedral : 17.261 173.531 5670 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.54 % Favored : 98.43 % Rotamer: Outliers : 2.90 % Allowed : 13.49 % Favored : 83.61 % 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: 1.49 (0.15), residues: 3130 helix: 2.01 (0.13), residues: 1537 sheet: 0.12 (0.24), residues: 466 loop : 0.04 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 362 TYR 0.017 0.002 TYR E 248 PHE 0.017 0.002 PHE B 226 TRP 0.019 0.002 TRP D 245 HIS 0.006 0.001 HIS E 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (29756) covalent geometry : angle 0.57885 / 0.31 (40938) hydrogen bonds : bond 0.05104 / 3.42 ( 1484) hydrogen bonds : angle 4.29221 / 3.11 ( 4064) metal coordination : bond 0.00515 / 0.30 ( 8) metal coordination : angle 2.21475 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 343 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7476 (mm-40) REVERT: A 177 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8286 (mtmm) REVERT: A 211 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7941 (ttmm) REVERT: A 219 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7601 (mtp-110) REVERT: A 245 GLU cc_start: 0.8533 (mt-10) cc_final: 0.7693 (mm-30) REVERT: B 23 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7504 (mtt90) REVERT: B 119 LYS cc_start: 0.8580 (mttt) cc_final: 0.8310 (mtmp) REVERT: B 138 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: B 170 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7528 (mp0) REVERT: B 279 MET cc_start: 0.3532 (tpp) cc_final: 0.2345 (ttm) REVERT: B 289 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.4092 (ttm) REVERT: B 320 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8288 (tttt) REVERT: B 404 LYS cc_start: 0.8927 (tttm) cc_final: 0.8343 (ttmt) REVERT: B 437 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8663 (ttmt) REVERT: B 479 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8525 (t) REVERT: B 496 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 499 ASN cc_start: 0.7328 (t0) cc_final: 0.7009 (t0) REVERT: B 533 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7635 (ttp-110) REVERT: B 536 LYS cc_start: 0.7484 (ttpp) cc_final: 0.6866 (pttt) REVERT: B 537 MET cc_start: 0.7597 (mmt) cc_final: 0.7360 (mmm) REVERT: C 68 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8155 (ttm-80) REVERT: C 136 ASP cc_start: 0.7512 (p0) cc_final: 0.7299 (p0) REVERT: C 152 LYS cc_start: 0.7890 (mttt) cc_final: 0.7633 (mppt) REVERT: C 155 LYS cc_start: 0.8320 (mttt) cc_final: 0.8045 (mttm) REVERT: C 216 LYS cc_start: 0.7837 (mmtt) cc_final: 0.6982 (mtpp) REVERT: C 318 VAL cc_start: 0.8770 (t) cc_final: 0.8483 (m) REVERT: C 383 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7854 (mp0) REVERT: C 404 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8610 (ttmt) REVERT: C 436 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8005 (mt-10) REVERT: D 41 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: D 155 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8341 (mtmp) REVERT: D 221 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7717 (mtp85) REVERT: D 279 MET cc_start: -0.0457 (mtt) cc_final: -0.0813 (tpt) REVERT: D 308 VAL cc_start: 0.6740 (m) cc_final: 0.6538 (t) REVERT: D 336 MET cc_start: 0.7297 (mmt) cc_final: 0.6767 (mpp) REVERT: D 450 ASP cc_start: 0.7626 (t0) cc_final: 0.7334 (t0) REVERT: D 466 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7661 (t0) REVERT: D 505 ASN cc_start: 0.6990 (t0) cc_final: 0.6299 (p0) REVERT: D 523 ILE cc_start: 0.8627 (tt) cc_final: 0.8327 (tp) REVERT: D 535 ASN cc_start: 0.7990 (m-40) cc_final: 0.7698 (m-40) REVERT: E 19 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: E 83 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8459 (ttpp) REVERT: E 138 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7893 (mp0) REVERT: E 140 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6840 (mmp-170) REVERT: E 143 ASP cc_start: 0.8884 (m-30) cc_final: 0.8670 (m-30) REVERT: E 244 GLU cc_start: 0.8810 (tt0) cc_final: 0.8461 (tm-30) REVERT: E 285 LEU cc_start: 0.5933 (mt) cc_final: 0.5666 (mt) REVERT: E 452 SER cc_start: 0.8505 (m) cc_final: 0.8300 (t) REVERT: E 471 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: E 474 MET cc_start: 0.8977 (mtt) cc_final: 0.8638 (mtt) REVERT: F 3 GLU cc_start: 0.7641 (tt0) cc_final: 0.7380 (tp30) REVERT: F 8 GLU cc_start: 0.6851 (tp30) cc_final: 0.6502 (pt0) REVERT: F 37 GLU cc_start: 0.7932 (tt0) cc_final: 0.7582 (mm-30) REVERT: F 82 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.6866 (mmt90) REVERT: F 104 ASP cc_start: 0.7097 (m-30) cc_final: 0.6293 (p0) REVERT: F 108 LYS cc_start: 0.8540 (tttt) cc_final: 0.7997 (tttm) REVERT: F 139 LYS cc_start: 0.7623 (ttmp) cc_final: 0.7222 (ttmt) REVERT: F 164 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7742 (tp-100) REVERT: F 182 GLU cc_start: 0.6659 (mm-30) cc_final: 0.5839 (tt0) REVERT: F 190 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.6687 (mmt180) REVERT: F 195 LYS cc_start: 0.6854 (tptm) cc_final: 0.5428 (ttpp) REVERT: G 52 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6805 (mtm-85) REVERT: G 94 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7845 (ttpt) REVERT: K 28 LYS cc_start: 0.5922 (mttp) cc_final: 0.5648 (mttt) REVERT: K 71 MET cc_start: 0.7469 (mmm) cc_final: 0.7096 (mmm) REVERT: K 115 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.4969 (mtt) REVERT: K 244 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7017 (mp0) REVERT: K 245 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6368 (mm-30) REVERT: K 274 LYS cc_start: 0.6134 (ttpp) cc_final: 0.5897 (ttpp) REVERT: K 301 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6237 (tp) outliers start: 80 outliers final: 23 residues processed: 388 average time/residue: 0.7596 time to fit residues: 336.6308 Evaluate side-chains 359 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 308 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 427 HIS C 499 ASN D 13 ASN D 212 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN E 427 HIS G 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116348 restraints weight = 62048.711| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.69 r_work: 0.2858 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29764 Z= 0.158 Angle : 0.571 10.882 40950 Z= 0.307 Chirality : 0.042 0.252 4616 Planarity : 0.004 0.048 4684 Dihedral : 17.157 171.835 5658 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.44 % Favored : 98.53 % Rotamer: Outliers : 2.40 % Allowed : 14.50 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3130 helix: 1.99 (0.13), residues: 1528 sheet: 0.07 (0.24), residues: 466 loop : -0.01 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 362 TYR 0.018 0.002 TYR C 104 PHE 0.018 0.002 PHE B 226 TRP 0.018 0.002 TRP D 245 HIS 0.004 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (29756) covalent geometry : angle 0.57025 / 0.31 (40938) hydrogen bonds : bond 0.04941 / 3.31 ( 1484) hydrogen bonds : angle 4.23037 / 3.06 ( 4064) metal coordination : bond 0.00544 / 0.33 ( 8) metal coordination : angle 1.93005 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7511 (mt0) REVERT: A 61 LEU cc_start: 0.8564 (mt) cc_final: 0.8325 (mp) REVERT: A 177 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8220 (mtmm) REVERT: A 211 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7912 (ttmm) REVERT: A 219 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7629 (mtp-110) REVERT: A 245 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7690 (mm-30) REVERT: B 119 LYS cc_start: 0.8646 (mttt) cc_final: 0.8354 (mtmp) REVERT: B 170 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7511 (mp0) REVERT: B 279 MET cc_start: 0.3858 (tpp) cc_final: 0.2522 (ttm) REVERT: B 289 MET cc_start: 0.4409 (OUTLIER) cc_final: 0.4075 (ttm) REVERT: B 320 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8287 (tttt) REVERT: B 404 LYS cc_start: 0.8937 (tttm) cc_final: 0.8343 (ttmt) REVERT: B 437 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8695 (ttmt) REVERT: B 474 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8600 (mtt) REVERT: B 496 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8067 (mp) REVERT: B 499 ASN cc_start: 0.7454 (t0) cc_final: 0.7098 (t0) REVERT: B 533 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7715 (ttp-110) REVERT: B 536 LYS cc_start: 0.7541 (ttpp) cc_final: 0.6923 (pttt) REVERT: B 537 MET cc_start: 0.7613 (mmt) cc_final: 0.7368 (mmm) REVERT: C 68 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8159 (ttm-80) REVERT: C 119 LYS cc_start: 0.7446 (ttpt) cc_final: 0.7129 (ttpp) REVERT: C 136 ASP cc_start: 0.7556 (p0) cc_final: 0.7333 (p0) REVERT: C 152 LYS cc_start: 0.7934 (mttt) cc_final: 0.7655 (mppt) REVERT: C 155 LYS cc_start: 0.8294 (mttt) cc_final: 0.7955 (mttm) REVERT: C 216 LYS cc_start: 0.7854 (mmtt) cc_final: 0.6984 (mtpp) REVERT: C 221 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7878 (mtp-110) REVERT: C 318 VAL cc_start: 0.8781 (t) cc_final: 0.8477 (m) REVERT: C 383 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7812 (mp0) REVERT: C 404 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8632 (ttmt) REVERT: C 436 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7935 (mt-10) REVERT: D 41 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: D 155 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8311 (mtmp) REVERT: D 224 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: D 279 MET cc_start: -0.0311 (mtt) cc_final: -0.0665 (tpt) REVERT: D 308 VAL cc_start: 0.6763 (m) cc_final: 0.6526 (t) REVERT: D 450 ASP cc_start: 0.7699 (t0) cc_final: 0.7387 (t0) REVERT: D 466 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7635 (t0) REVERT: D 505 ASN cc_start: 0.7020 (t0) cc_final: 0.6332 (p0) REVERT: D 523 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8386 (tp) REVERT: D 535 ASN cc_start: 0.8059 (m-40) cc_final: 0.7786 (m-40) REVERT: E 19 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: E 83 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8480 (ttpp) REVERT: E 138 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7879 (mp0) REVERT: E 244 GLU cc_start: 0.8778 (tt0) cc_final: 0.8420 (tm-30) REVERT: E 452 SER cc_start: 0.8541 (m) cc_final: 0.8302 (t) REVERT: E 471 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: E 474 MET cc_start: 0.8969 (mtt) cc_final: 0.8634 (mtt) REVERT: F 3 GLU cc_start: 0.7647 (tt0) cc_final: 0.7383 (tp30) REVERT: F 8 GLU cc_start: 0.6961 (tp30) cc_final: 0.6459 (pt0) REVERT: F 37 GLU cc_start: 0.7961 (tt0) cc_final: 0.7640 (mm-30) REVERT: F 63 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7815 (mmmm) REVERT: F 82 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6845 (mmt90) REVERT: F 104 ASP cc_start: 0.7022 (m-30) cc_final: 0.6262 (p0) REVERT: F 108 LYS cc_start: 0.8439 (tttt) cc_final: 0.7996 (tttm) REVERT: F 112 GLU cc_start: 0.6740 (mp0) cc_final: 0.6284 (pm20) REVERT: F 139 LYS cc_start: 0.7630 (ttmp) cc_final: 0.7276 (ttmt) REVERT: F 182 GLU cc_start: 0.6677 (mm-30) cc_final: 0.5849 (tt0) REVERT: F 190 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.6759 (mmt180) REVERT: F 195 LYS cc_start: 0.6762 (tptm) cc_final: 0.5374 (ttpp) REVERT: G 52 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6763 (mtm-85) REVERT: K 21 PHE cc_start: 0.5863 (t80) cc_final: 0.5368 (t80) REVERT: K 28 LYS cc_start: 0.5971 (mttp) cc_final: 0.5706 (mttt) REVERT: K 71 MET cc_start: 0.7546 (mmm) cc_final: 0.7150 (mmm) REVERT: K 115 MET cc_start: 0.5759 (mpt) cc_final: 0.4803 (mtt) REVERT: K 245 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6459 (mm-30) REVERT: K 274 LYS cc_start: 0.6262 (ttpp) cc_final: 0.5975 (ttpp) REVERT: K 301 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6444 (tp) outliers start: 65 outliers final: 22 residues processed: 362 average time/residue: 0.7437 time to fit residues: 307.6336 Evaluate side-chains 351 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 311 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 0.0770 chunk 74 optimal weight: 5.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS D 13 ASN D 212 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 ASN E 13 ASN G 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120265 restraints weight = 62681.354| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.62 r_work: 0.2930 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29764 Z= 0.107 Angle : 0.498 9.800 40950 Z= 0.270 Chirality : 0.039 0.166 4616 Planarity : 0.003 0.054 4684 Dihedral : 16.981 171.863 5657 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.65 % Rotamer: Outliers : 2.11 % Allowed : 14.96 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 3130 helix: 2.16 (0.13), residues: 1545 sheet: -0.02 (0.24), residues: 466 loop : 0.05 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 362 TYR 0.019 0.001 TYR E 248 PHE 0.017 0.001 PHE F 64 TRP 0.020 0.001 TRP D 245 HIS 0.005 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (29756) covalent geometry : angle 0.49710 / 0.27 (40938) hydrogen bonds : bond 0.03848 / 2.60 ( 1484) hydrogen bonds : angle 4.03536 / 2.92 ( 4064) metal coordination : bond 0.00490 / 0.28 ( 8) metal coordination : angle 1.88611 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8517 (mt) cc_final: 0.8286 (mp) REVERT: A 177 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8126 (mtmm) REVERT: A 211 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7876 (ttmm) REVERT: A 219 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7609 (mtp-110) REVERT: A 245 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7636 (mm-30) REVERT: B 119 LYS cc_start: 0.8561 (mttt) cc_final: 0.8279 (tptp) REVERT: B 138 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: B 170 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7474 (mp0) REVERT: B 289 MET cc_start: 0.4584 (ttm) cc_final: 0.4177 (ttm) REVERT: B 320 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8307 (tttt) REVERT: B 404 LYS cc_start: 0.8854 (tttm) cc_final: 0.8272 (ttmt) REVERT: B 474 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8563 (mtt) REVERT: B 479 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8476 (t) REVERT: B 499 ASN cc_start: 0.7116 (t0) cc_final: 0.6752 (t0) REVERT: B 533 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7575 (ttp-110) REVERT: B 536 LYS cc_start: 0.7469 (ttpp) cc_final: 0.6829 (pttt) REVERT: B 537 MET cc_start: 0.7582 (mmt) cc_final: 0.6949 (mpp) REVERT: C 68 ARG cc_start: 0.8319 (ttm170) cc_final: 0.8013 (ttm110) REVERT: C 136 ASP cc_start: 0.7555 (p0) cc_final: 0.7308 (p0) REVERT: C 140 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6937 (mmt180) REVERT: C 152 LYS cc_start: 0.7976 (mttt) cc_final: 0.7671 (mppt) REVERT: C 155 LYS cc_start: 0.8239 (mttt) cc_final: 0.7907 (mttm) REVERT: C 216 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7022 (mtpp) REVERT: C 318 VAL cc_start: 0.8650 (t) cc_final: 0.8326 (m) REVERT: C 383 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7784 (mp0) REVERT: C 404 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8581 (ttmt) REVERT: C 436 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7958 (mt-10) REVERT: D 41 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: D 155 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8255 (mtmp) REVERT: D 224 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: D 279 MET cc_start: -0.0385 (mtt) cc_final: -0.0677 (tpt) REVERT: D 308 VAL cc_start: 0.6744 (m) cc_final: 0.6480 (t) REVERT: D 336 MET cc_start: 0.6986 (mmt) cc_final: 0.6726 (mpp) REVERT: D 450 ASP cc_start: 0.7685 (t0) cc_final: 0.7279 (t0) REVERT: D 505 ASN cc_start: 0.6948 (t0) cc_final: 0.6392 (p0) REVERT: D 523 ILE cc_start: 0.8608 (tt) cc_final: 0.8359 (tp) REVERT: D 535 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7690 (m-40) REVERT: E 83 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8487 (ttpp) REVERT: E 138 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7937 (mp0) REVERT: E 206 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: E 244 GLU cc_start: 0.8792 (tt0) cc_final: 0.8429 (tm-30) REVERT: E 452 SER cc_start: 0.8551 (m) cc_final: 0.8347 (t) REVERT: E 471 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: E 474 MET cc_start: 0.8932 (mtt) cc_final: 0.8590 (mtt) REVERT: E 533 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.6553 (mtm180) REVERT: F 3 GLU cc_start: 0.7683 (tt0) cc_final: 0.7395 (tp30) REVERT: F 8 GLU cc_start: 0.6864 (tp30) cc_final: 0.6400 (pt0) REVERT: F 37 GLU cc_start: 0.7879 (tt0) cc_final: 0.7607 (mm-30) REVERT: F 82 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6875 (mmt90) REVERT: F 104 ASP cc_start: 0.7104 (m-30) cc_final: 0.6316 (p0) REVERT: F 112 GLU cc_start: 0.6717 (mp0) cc_final: 0.6335 (pm20) REVERT: F 139 LYS cc_start: 0.7562 (ttmp) cc_final: 0.7213 (ttmt) REVERT: F 182 GLU cc_start: 0.6656 (mm-30) cc_final: 0.5877 (tt0) REVERT: F 190 ARG cc_start: 0.7640 (mtt-85) cc_final: 0.6753 (mmt180) REVERT: F 195 LYS cc_start: 0.6683 (tptm) cc_final: 0.5321 (ttpp) REVERT: G 52 ARG cc_start: 0.7138 (mtt90) cc_final: 0.6706 (mtm-85) REVERT: G 190 ARG cc_start: 0.6884 (mtm110) cc_final: 0.6658 (mtm110) REVERT: K 21 PHE cc_start: 0.5872 (t80) cc_final: 0.5329 (t80) REVERT: K 29 TYR cc_start: 0.6886 (m-80) cc_final: 0.6483 (m-80) REVERT: K 71 MET cc_start: 0.7540 (mmm) cc_final: 0.7114 (mmm) REVERT: K 115 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.4872 (mtt) REVERT: K 219 ARG cc_start: 0.7736 (mtp85) cc_final: 0.6467 (mtm-85) REVERT: K 245 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6467 (mm-30) REVERT: K 274 LYS cc_start: 0.6252 (ttpp) cc_final: 0.5954 (ttpp) REVERT: K 301 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6351 (tp) outliers start: 57 outliers final: 12 residues processed: 366 average time/residue: 0.7739 time to fit residues: 324.1423 Evaluate side-chains 349 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 321 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 322 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 427 HIS ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN D 95 ASN D 212 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121021 restraints weight = 56923.548| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.55 r_work: 0.2901 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29764 Z= 0.119 Angle : 0.505 9.304 40950 Z= 0.274 Chirality : 0.039 0.168 4616 Planarity : 0.004 0.049 4684 Dihedral : 16.939 171.650 5649 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.38 % Favored : 98.59 % Rotamer: Outliers : 1.68 % Allowed : 15.82 % Favored : 82.50 % 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: 1.62 (0.15), residues: 3130 helix: 2.20 (0.13), residues: 1533 sheet: -0.02 (0.24), residues: 454 loop : 0.06 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 362 TYR 0.017 0.001 TYR B 104 PHE 0.016 0.001 PHE B 242 TRP 0.017 0.001 TRP D 245 HIS 0.006 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (29756) covalent geometry : angle 0.50413 / 0.27 (40938) hydrogen bonds : bond 0.04058 / 2.72 ( 1484) hydrogen bonds : angle 4.02494 / 2.91 ( 4064) metal coordination : bond 0.00489 / 0.29 ( 8) metal coordination : angle 1.72936 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 317 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 38 THR cc_start: 0.8789 (p) cc_final: 0.8557 (p) REVERT: A 61 LEU cc_start: 0.8546 (mt) cc_final: 0.8325 (mp) REVERT: A 177 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8132 (mtmm) REVERT: A 211 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7925 (ttmm) REVERT: A 219 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7564 (mtp-110) REVERT: A 245 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7648 (mm-30) REVERT: B 119 LYS cc_start: 0.8566 (mttt) cc_final: 0.8319 (tptp) REVERT: B 170 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7497 (mp0) REVERT: B 279 MET cc_start: 0.3671 (tpp) cc_final: 0.2645 (ttm) REVERT: B 289 MET cc_start: 0.4549 (ttm) cc_final: 0.4126 (ttm) REVERT: B 320 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8333 (tttt) REVERT: B 404 LYS cc_start: 0.8862 (tttm) cc_final: 0.8289 (ttmt) REVERT: B 437 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8753 (ttmt) REVERT: B 474 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8564 (mtt) REVERT: B 479 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8488 (t) REVERT: B 499 ASN cc_start: 0.7203 (t0) cc_final: 0.6785 (t0) REVERT: B 536 LYS cc_start: 0.7520 (ttpp) cc_final: 0.6909 (pttt) REVERT: B 537 MET cc_start: 0.7621 (mmt) cc_final: 0.7352 (mmm) REVERT: C 68 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8062 (ttm110) REVERT: C 126 ARG cc_start: 0.8395 (mtp85) cc_final: 0.8183 (mtp180) REVERT: C 136 ASP cc_start: 0.7622 (p0) cc_final: 0.7353 (p0) REVERT: C 140 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6897 (mmm160) REVERT: C 152 LYS cc_start: 0.8011 (mttt) cc_final: 0.7688 (mppt) REVERT: C 155 LYS cc_start: 0.8226 (mttt) cc_final: 0.7942 (mttm) REVERT: C 216 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7015 (mtpp) REVERT: C 318 VAL cc_start: 0.8663 (t) cc_final: 0.8343 (m) REVERT: C 383 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7812 (mp0) REVERT: C 404 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: C 436 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7940 (mt-10) REVERT: D 41 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: D 224 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: D 279 MET cc_start: -0.0456 (mtt) cc_final: -0.0724 (tpt) REVERT: D 308 VAL cc_start: 0.6788 (m) cc_final: 0.6449 (t) REVERT: D 336 MET cc_start: 0.6999 (mmt) cc_final: 0.6739 (mpp) REVERT: D 450 ASP cc_start: 0.7669 (t0) cc_final: 0.7207 (t0) REVERT: D 474 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7543 (mtt) REVERT: D 505 ASN cc_start: 0.7073 (t0) cc_final: 0.6341 (p0) REVERT: D 523 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (tp) REVERT: D 535 ASN cc_start: 0.8087 (m-40) cc_final: 0.7811 (m-40) REVERT: E 83 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (ttpp) REVERT: E 138 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7964 (mp0) REVERT: E 244 GLU cc_start: 0.8862 (tt0) cc_final: 0.8498 (tm-30) REVERT: E 452 SER cc_start: 0.8541 (m) cc_final: 0.8335 (t) REVERT: E 471 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: E 474 MET cc_start: 0.8926 (mtt) cc_final: 0.8582 (mtt) REVERT: E 533 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.6634 (mtm180) REVERT: F 3 GLU cc_start: 0.7699 (tt0) cc_final: 0.7403 (tp30) REVERT: F 8 GLU cc_start: 0.6887 (tp30) cc_final: 0.6339 (pt0) REVERT: F 37 GLU cc_start: 0.7934 (tt0) cc_final: 0.7610 (mm-30) REVERT: F 82 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6894 (mmt90) REVERT: F 104 ASP cc_start: 0.7073 (m-30) cc_final: 0.6236 (p0) REVERT: F 139 LYS cc_start: 0.7549 (ttmp) cc_final: 0.7304 (ttmt) REVERT: F 182 GLU cc_start: 0.6599 (mm-30) cc_final: 0.5844 (tt0) REVERT: F 190 ARG cc_start: 0.7643 (mtt-85) cc_final: 0.6714 (mmt180) REVERT: F 195 LYS cc_start: 0.6692 (tptm) cc_final: 0.5299 (ttpp) REVERT: G 52 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6774 (mtm-85) REVERT: G 194 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6172 (tt0) REVERT: K 21 PHE cc_start: 0.6022 (t80) cc_final: 0.5504 (t80) REVERT: K 29 TYR cc_start: 0.6899 (m-80) cc_final: 0.6478 (m-80) REVERT: K 71 MET cc_start: 0.7480 (mmm) cc_final: 0.7095 (mmm) REVERT: K 115 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.4887 (mtt) REVERT: K 219 ARG cc_start: 0.7779 (mtp85) cc_final: 0.6509 (mtm-85) REVERT: K 245 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6458 (mm-30) REVERT: K 274 LYS cc_start: 0.6187 (ttpp) cc_final: 0.5909 (ttpp) outliers start: 45 outliers final: 17 residues processed: 346 average time/residue: 0.7959 time to fit residues: 315.5212 Evaluate side-chains 341 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 309 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 290 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 175 optimal weight: 2.9990 chunk 288 optimal weight: 20.0000 chunk 61 optimal weight: 0.3980 chunk 206 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 212 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 ASN G 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122299 restraints weight = 63169.793| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.52 r_work: 0.2912 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29764 Z= 0.112 Angle : 0.494 9.295 40950 Z= 0.267 Chirality : 0.039 0.163 4616 Planarity : 0.003 0.050 4684 Dihedral : 16.897 171.819 5649 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.38 % Favored : 98.59 % Rotamer: Outliers : 1.93 % Allowed : 15.89 % Favored : 82.18 % 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: 1.68 (0.15), residues: 3130 helix: 2.27 (0.13), residues: 1533 sheet: -0.04 (0.24), residues: 454 loop : 0.09 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 362 TYR 0.017 0.001 TYR G 117 PHE 0.014 0.001 PHE K 21 TRP 0.017 0.001 TRP D 245 HIS 0.006 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (29756) covalent geometry : angle 0.49323 / 0.27 (40938) hydrogen bonds : bond 0.03892 / 2.62 ( 1484) hydrogen bonds : angle 3.98073 / 2.88 ( 4064) metal coordination : bond 0.00470 / 0.28 ( 8) metal coordination : angle 1.78159 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6260 Ramachandran restraints generated. 3130 Oldfield, 0 Emsley, 3130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 319 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.8785 (p) cc_final: 0.8560 (p) REVERT: A 61 LEU cc_start: 0.8582 (mt) cc_final: 0.8360 (mp) REVERT: A 142 ARG cc_start: 0.7691 (ptp90) cc_final: 0.7440 (ptt90) REVERT: A 177 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8130 (mtmm) REVERT: A 211 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7941 (ttmm) REVERT: A 219 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7659 (mtp-110) REVERT: A 245 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7636 (mm-30) REVERT: B 119 LYS cc_start: 0.8522 (mttt) cc_final: 0.8279 (tptp) REVERT: B 170 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7530 (mp0) REVERT: B 279 MET cc_start: 0.3731 (tpp) cc_final: 0.2661 (ttm) REVERT: B 289 MET cc_start: 0.4589 (ttm) cc_final: 0.4156 (ttm) REVERT: B 320 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8357 (tttt) REVERT: B 404 LYS cc_start: 0.8872 (tttm) cc_final: 0.8314 (ttmt) REVERT: B 437 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8749 (ttmt) REVERT: B 474 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8568 (mtt) REVERT: B 479 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8500 (t) REVERT: B 496 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 499 ASN cc_start: 0.7241 (t0) cc_final: 0.6901 (t0) REVERT: B 533 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7546 (mtm-85) REVERT: B 536 LYS cc_start: 0.7556 (ttpp) cc_final: 0.6943 (pttt) REVERT: B 537 MET cc_start: 0.7636 (mmt) cc_final: 0.7400 (mmm) REVERT: C 68 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8067 (ttm110) REVERT: C 136 ASP cc_start: 0.7555 (p0) cc_final: 0.7302 (p0) REVERT: C 140 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6986 (mmm160) REVERT: C 152 LYS cc_start: 0.8000 (mttt) cc_final: 0.7710 (mppt) REVERT: C 155 LYS cc_start: 0.8197 (mttt) cc_final: 0.7928 (mttm) REVERT: C 216 LYS cc_start: 0.7860 (mmtt) cc_final: 0.6992 (mtpp) REVERT: C 279 MET cc_start: 0.1080 (tmm) cc_final: -0.0065 (ptm) REVERT: C 318 VAL cc_start: 0.8666 (t) cc_final: 0.8343 (m) REVERT: C 404 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8622 (ttmt) REVERT: C 436 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7966 (mt-10) REVERT: D 41 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: D 155 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8305 (mtmp) REVERT: D 224 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: D 279 MET cc_start: -0.0350 (mtt) cc_final: -0.0700 (tpt) REVERT: D 308 VAL cc_start: 0.6766 (m) cc_final: 0.6398 (t) REVERT: D 450 ASP cc_start: 0.7771 (t0) cc_final: 0.7286 (t0) REVERT: D 474 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.7511 (mtt) REVERT: D 505 ASN cc_start: 0.7049 (t0) cc_final: 0.6391 (p0) REVERT: D 523 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8426 (tp) REVERT: E 83 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (ttpp) REVERT: E 138 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8000 (mp0) REVERT: E 244 GLU cc_start: 0.8793 (tt0) cc_final: 0.8436 (tm-30) REVERT: E 452 SER cc_start: 0.8563 (m) cc_final: 0.8346 (t) REVERT: E 471 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: E 474 MET cc_start: 0.8903 (mtt) cc_final: 0.8558 (mtt) REVERT: E 533 ARG cc_start: 0.7292 (ttm-80) cc_final: 0.6655 (mtm180) REVERT: F 3 GLU cc_start: 0.7721 (tt0) cc_final: 0.7450 (tp30) REVERT: F 8 GLU cc_start: 0.6877 (tp30) cc_final: 0.6295 (pt0) REVERT: F 37 GLU cc_start: 0.7895 (tt0) cc_final: 0.7661 (mm-30) REVERT: F 82 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6910 (mmt90) REVERT: F 104 ASP cc_start: 0.7124 (m-30) cc_final: 0.6287 (p0) REVERT: F 139 LYS cc_start: 0.7661 (ttmp) cc_final: 0.7271 (ttmt) REVERT: F 182 GLU cc_start: 0.6714 (mm-30) cc_final: 0.5965 (tt0) REVERT: F 190 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.6830 (mmt180) REVERT: F 195 LYS cc_start: 0.6691 (tptm) cc_final: 0.5381 (ttpp) REVERT: G 52 ARG cc_start: 0.7162 (mtt90) cc_final: 0.6831 (mtm-85) REVERT: G 194 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6111 (tt0) REVERT: K 21 PHE cc_start: 0.6290 (t80) cc_final: 0.5759 (t80) REVERT: K 29 TYR cc_start: 0.6987 (m-80) cc_final: 0.6543 (m-80) REVERT: K 71 MET cc_start: 0.7584 (mmm) cc_final: 0.7207 (mmm) REVERT: K 115 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.4880 (mtt) REVERT: K 219 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7381 (mmm160) REVERT: K 274 LYS cc_start: 0.6293 (ttpp) cc_final: 0.6003 (ttpp) outliers start: 52 outliers final: 21 residues processed: 348 average time/residue: 0.8004 time to fit residues: 318.6474 Evaluate side-chains 341 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 290 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5434 > 50: distance: 31 - 49: 3.141 distance: 43 - 49: 6.427 distance: 49 - 50: 3.432 distance: 50 - 51: 5.011 distance: 51 - 52: 5.110 distance: 51 - 57: 3.493 distance: 53 - 54: 7.987 distance: 54 - 56: 11.505 distance: 58 - 59: 4.813 distance: 58 - 61: 8.225 distance: 59 - 66: 4.584 distance: 61 - 62: 13.640 distance: 62 - 63: 7.288 distance: 63 - 64: 16.540 distance: 64 - 65: 36.930 distance: 67 - 68: 4.405 distance: 70 - 71: 3.566 distance: 71 - 72: 9.057 distance: 71 - 73: 5.692 distance: 74 - 75: 7.798 distance: 75 - 78: 7.089 distance: 76 - 77: 12.685 distance: 76 - 83: 8.159 distance: 78 - 79: 13.016 distance: 79 - 80: 9.028 distance: 80 - 81: 10.989 distance: 80 - 82: 9.648 distance: 83 - 84: 13.805 distance: 84 - 85: 11.827 distance: 84 - 87: 4.414 distance: 85 - 86: 15.771 distance: 85 - 92: 40.758 distance: 87 - 88: 24.447 distance: 88 - 89: 21.919 distance: 89 - 90: 16.938 distance: 89 - 91: 16.056 distance: 92 - 93: 7.529 distance: 93 - 94: 23.496 distance: 93 - 96: 4.891 distance: 94 - 95: 9.209 distance: 94 - 100: 9.232 distance: 96 - 97: 13.300 distance: 97 - 98: 8.205 distance: 97 - 99: 3.305 distance: 100 - 101: 7.258 distance: 101 - 102: 3.830 distance: 101 - 104: 3.700 distance: 102 - 103: 11.466 distance: 102 - 108: 4.013 distance: 104 - 105: 5.116 distance: 105 - 106: 6.582 distance: 105 - 107: 10.782 distance: 108 - 109: 5.740 distance: 108 - 170: 10.150 distance: 110 - 111: 5.022 distance: 110 - 115: 3.423 distance: 111 - 182: 6.981 distance: 112 - 113: 4.571 distance: 112 - 114: 11.401 distance: 116 - 117: 6.878 distance: 116 - 119: 3.884 distance: 117 - 118: 7.440 distance: 117 - 122: 6.970 distance: 119 - 120: 6.474 distance: 119 - 121: 4.640 distance: 122 - 123: 4.512 distance: 122 - 185: 4.331 distance: 123 - 124: 5.365 distance: 123 - 126: 4.524 distance: 124 - 125: 5.337 distance: 124 - 130: 3.017 distance: 126 - 127: 4.953 distance: 126 - 128: 4.266 distance: 127 - 129: 5.817