Starting phenix.real_space_refine on Fri Feb 6 14:01:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kk1_62381/02_2026/9kk1_62381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kk1_62381/02_2026/9kk1_62381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kk1_62381/02_2026/9kk1_62381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kk1_62381/02_2026/9kk1_62381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kk1_62381/02_2026/9kk1_62381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kk1_62381/02_2026/9kk1_62381.map" } resolution = 2.71 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= 0.019 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 120 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 15539 2.51 5 N 4444 2.21 5 O 5088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25276 Number of models: 1 Model: "" Number of chains: 15 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: 4259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 530, 4248 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 15, 'TRANS': 514} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 530, 4248 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 15, 'TRANS': 514} Chain breaks: 2 bond proxies already assigned to first conformer: 4307 Chain: "C" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4269 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 15, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 4317 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 4284 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 4284 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 bond proxies already assigned to first conformer: 4317 Chain: "E" Number of atoms: 4102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 508, 4072 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 508, 4072 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 4 bond proxies already assigned to first conformer: 4103 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19773 SG CYS F 43 33.351 119.388 111.057 1.00 73.19 S ATOM 19796 SG CYS F 46 35.429 116.484 112.288 1.00 69.33 S ATOM 20067 SG CYS F 78 35.470 117.102 108.710 1.00 76.46 S ATOM 20156 SG CYS F 90 32.737 115.391 110.135 1.00 73.21 S ATOM 21474 SG CYS G 43 34.475 28.622 49.435 1.00 79.69 S ATOM 21497 SG CYS G 46 36.339 31.181 47.357 1.00 71.96 S ATOM 21768 SG CYS G 78 36.681 31.464 50.969 1.00 87.15 S ATOM 21857 SG CYS G 90 33.790 32.742 49.456 1.00 79.29 S Residues with excluded nonbonded symmetry interactions: 5 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 residue: pdb=" N AASN D 466 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 466 " occ=0.50 residue: pdb=" N AGLN E 361 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN E 361 " occ=0.50 residue: pdb=" N ATRP E 405 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP E 405 " occ=0.50 Time building chain proxies: 8.46, per 1000 atoms: 0.33 Number of scatterers: 25276 At special positions: 0 Unit cell: (130.476, 149.4, 162.348, 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 82 16.00 P 120 15.00 Mg 1 11.99 O 5088 8.00 N 4444 7.00 C 15539 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: 2.20 Conformation dependent library (CDL) restraints added in 1.7 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 46 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb=" ZN G 301 " 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 46 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " Number of angles added : 12 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 23 sheets defined 54.4% alpha, 12.4% beta 42 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 3.26 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: 4.325A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.586A 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 197 through 200 removed outlier: 3.503A pdb=" N LYS A 200 " --> pdb=" O ASP A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 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: 3.791A 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: 3.926A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.118A 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 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 547 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: 3.917A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.075A 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: 3.617A pdb=" N GLU C 223 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 6.190A 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: 3.599A 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 545 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: 3.717A pdb=" N LYS D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.090A 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 545 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: 3.889A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.085A 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 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: 4.163A pdb=" N ASN E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 413 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 4.463A 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 547 Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.992A pdb=" N GLN F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 16' Processing helix chain 'F' and resid 22 through 26 Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.712A pdb=" N LEU F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 113 through 116 removed outlier: 3.708A 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: 3.869A pdb=" N ILE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Proline residue: F 168 - end of helix removed outlier: 3.526A pdb=" N TYR F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 176 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'G' and resid 11 through 16 removed outlier: 3.989A pdb=" N GLN G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 11 through 16' Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 31 through 40 removed outlier: 3.731A pdb=" N LEU G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 113 through 116 removed outlier: 3.702A 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: 3.867A pdb=" N ILE G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 3.528A pdb=" N TYR G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 176 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 Processing helix chain 'G' and resid 201 through 210 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 234 through 236 removed outlier: 4.547A pdb=" N ARG A 234 " --> pdb=" O ILE A 241 " (cutoff:3.500A) 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: 6.469A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE B 74 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 10.693A 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: 6.759A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.314A 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: 3.892A 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: 6.446A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU C 66 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 149 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE C 74 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N TYR C 141 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE C 150 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.942A 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: 6.342A pdb=" N THR C 199 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU C 393 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 201 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.400A 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: 3.847A 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: 6.473A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 66 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE D 149 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE D 74 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N TYR D 141 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE D 150 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.925A 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: 6.339A pdb=" N THR D 199 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU D 393 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 201 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY D 390 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE D 423 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.376A 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: 3.859A pdb=" N ASN D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 337 " --> pdb=" O SER D 340 " (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: 6.432A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 66 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE E 149 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N TYR E 141 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE E 150 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.917A 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: 6.294A pdb=" N THR E 199 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU E 393 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA E 201 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.311A 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: 3.881A 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 1189 hydrogen bonds defined for protein. 3386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4374 1.33 - 1.45: 7290 1.45 - 1.57: 13917 1.57 - 1.69: 273 1.69 - 1.81: 137 Bond restraints: 25991 Sorted by residual: bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C5 ADP E 601 " pdb=" C6 ADP E 601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 ADP C 601 " pdb=" C6 ADP C 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 25986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 33378 3.37 - 6.75: 2010 6.75 - 10.12: 230 10.12 - 13.50: 9 13.50 - 16.87: 2 Bond angle restraints: 35629 Sorted by residual: angle pdb=" O3' A H 42 " pdb=" P A H 43 " pdb=" O5' A H 43 " ideal model delta sigma weight residual 104.00 87.13 16.87 1.50e+00 4.44e-01 1.26e+02 angle pdb=" O3' A H 47 " pdb=" P U H 48 " pdb=" O5' U H 48 " ideal model delta sigma weight residual 104.00 90.40 13.60 1.50e+00 4.44e-01 8.22e+01 angle pdb=" CA PHE B 453 " pdb=" CB PHE B 453 " pdb=" CG PHE B 453 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.85e+01 angle pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " pdb=" CG ASP A 17 " ideal model delta sigma weight residual 112.60 120.81 -8.21 1.00e+00 1.00e+00 6.74e+01 angle pdb=" CA ASP B 458 " pdb=" CB ASP B 458 " pdb=" CG ASP B 458 " ideal model delta sigma weight residual 112.60 120.72 -8.12 1.00e+00 1.00e+00 6.60e+01 ... (remaining 35624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 14233 23.80 - 47.61: 976 47.61 - 71.41: 324 71.41 - 95.21: 69 95.21 - 119.02: 1 Dihedral angle restraints: 15603 sinusoidal: 7343 harmonic: 8260 Sorted by residual: 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 -139.99 17.39 0 2.50e+00 1.60e-01 4.84e+01 dihedral pdb=" N ASP A 17 " pdb=" C ASP A 17 " pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " ideal model delta harmonic sigma weight residual 122.80 138.38 -15.58 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 -179.02 119.02 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 15600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3492 0.132 - 0.263: 468 0.263 - 0.395: 19 0.395 - 0.527: 2 0.527 - 0.658: 3 Chirality restraints: 3984 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 2.35 -3.00 -0.66 2.00e-01 2.50e+01 1.08e+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 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P U H 18 " pdb=" OP1 U H 18 " pdb=" OP2 U H 18 " pdb=" O5' U H 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.47e+00 ... (remaining 3981 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G H 23 " -0.081 2.00e-02 2.50e+03 3.31e-02 3.28e+01 pdb=" N9 G H 23 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G H 23 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G H 23 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G H 23 " 0.011 2.00e-02 2.50e+03 pdb=" C6 G H 23 " -0.033 2.00e-02 2.50e+03 pdb=" O6 G H 23 " -0.018 2.00e-02 2.50e+03 pdb=" N1 G H 23 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G H 23 " 0.015 2.00e-02 2.50e+03 pdb=" N2 G H 23 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G H 23 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G H 23 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 245 " -0.067 2.00e-02 2.50e+03 3.40e-02 2.89e+01 pdb=" CG TRP C 245 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 245 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 245 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP C 245 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 245 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 245 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 245 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 245 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 245 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 18 " 0.064 2.00e-02 2.50e+03 3.08e-02 2.38e+01 pdb=" N1 DT I 18 " -0.060 2.00e-02 2.50e+03 pdb=" C2 DT I 18 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT I 18 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 18 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DT I 18 " 0.013 2.00e-02 2.50e+03 pdb=" O4 DT I 18 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DT I 18 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 18 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 18 " -0.026 2.00e-02 2.50e+03 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 475 2.69 - 3.24: 22693 3.24 - 3.79: 41788 3.79 - 4.35: 56476 4.35 - 4.90: 88821 Nonbonded interactions: 210253 Sorted by model distance: nonbonded pdb=" OD1 ASP A 187 " pdb=" O3' DC I 77 " model vdw 2.136 3.040 nonbonded pdb=" O PHE E 200 " pdb=" OG1 THR E 232 " model vdw 2.176 3.040 nonbonded pdb=" OD1 ASP C 184 " pdb=" NH1 ARG C 187 " model vdw 2.224 3.120 nonbonded pdb=" OG1 THR E 194 " pdb=" O VAL E 304 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP D 184 " pdb=" NH1 ARG D 187 " model vdw 2.260 3.120 ... (remaining 210248 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 'B' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 255 or resid 259 through 275 or \ resid 280 through 360 or resid 362 through 401 or resid 403 through 404 or resi \ d 406 through 426 or resid 428 through 465 or resid 467 through 545)) selection = (chain 'C' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 255 or resid 259 through 275 or \ resid 280 through 302 or resid 308 through 360 or resid 362 through 401 or resi \ d 403 through 404 or resid 406 through 426 or resid 428 through 465 or resid 467 \ through 545)) selection = (chain 'D' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 255 or resid 259 through 275 or \ resid 280 through 302 or resid 308 through 360 or resid 362 through 401 or resi \ d 403 through 404 or resid 406 through 426 or resid 428 through 465 or resid 467 \ through 545)) selection = (chain 'E' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 302 or resid 308 through 360 or \ resid 362 through 401 or resid 403 through 404 or resid 406 through 426 or resi \ d 428 through 465 or resid 467 through 545)) } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 6.020 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 33.530 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 0.112 25999 Z= 0.625 Angle : 1.803 17.978 35641 Z= 1.122 Chirality : 0.089 0.658 3984 Planarity : 0.007 0.082 4197 Dihedral : 18.122 119.015 10249 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.36 % Rotamer: Outliers : 3.57 % Allowed : 5.79 % Favored : 90.64 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 2822 helix: 1.02 (0.13), residues: 1324 sheet: 0.22 (0.26), residues: 381 loop : -0.08 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.005 ARG D 171 TYR 0.035 0.006 TYR E 248 PHE 0.028 0.005 PHE A 191 TRP 0.067 0.008 TRP C 245 HIS 0.015 0.003 HIS E 400 Details of bonding type rmsd covalent geometry : bond 0.01051 (25991) covalent geometry : angle 1.79524 (35629) hydrogen bonds : bond 0.18052 ( 1295) hydrogen bonds : angle 6.04548 ( 3574) metal coordination : bond 0.01077 ( 8) metal coordination : angle 9.44280 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 481 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.7513 (t) cc_final: 0.7233 (t) REVERT: A 75 LYS cc_start: 0.8422 (tppp) cc_final: 0.8186 (mptp) REVERT: A 207 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 301 LEU cc_start: 0.7938 (tp) cc_final: 0.7536 (tt) REVERT: A 304 MET cc_start: 0.7782 (mmm) cc_final: 0.7574 (mmm) REVERT: B 2 THR cc_start: 0.8008 (p) cc_final: 0.7675 (t) REVERT: B 94 ASN cc_start: 0.8488 (m-40) cc_final: 0.8232 (m110) REVERT: B 119 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8568 (ttmt) REVERT: B 143 ASP cc_start: 0.8621 (m-30) cc_final: 0.8390 (m-30) REVERT: B 224 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7339 (pt0) REVERT: B 279 MET cc_start: 0.2044 (mtt) cc_final: 0.1561 (mtt) REVERT: B 354 ILE cc_start: 0.8793 (mm) cc_final: 0.8580 (mp) REVERT: B 404 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8039 (tptp) REVERT: B 414 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8352 (mtp85) REVERT: B 465 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: B 536 LYS cc_start: 0.7103 (mttt) cc_final: 0.6832 (mttp) REVERT: C 42 MET cc_start: 0.7373 (mtp) cc_final: 0.6884 (mpt) REVERT: C 67 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7889 (ttp80) REVERT: C 126 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7619 (mtp180) REVERT: C 336 MET cc_start: 0.7286 (tpp) cc_final: 0.6358 (mpt) REVERT: C 414 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7204 (mtp85) REVERT: C 436 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 526 LYS cc_start: 0.7414 (mttp) cc_final: 0.7189 (mtpp) REVERT: D 285 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4805 (pp) REVERT: D 320 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7374 (mmtt) REVERT: D 396 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7512 (tt0) REVERT: D 450 ASP cc_start: 0.7873 (t70) cc_final: 0.7225 (t0) REVERT: D 455 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7332 (p0) REVERT: D 474 MET cc_start: 0.8664 (mtp) cc_final: 0.8187 (mtt) REVERT: D 496 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7408 (mp) REVERT: D 530 SER cc_start: 0.8050 (t) cc_final: 0.7827 (m) REVERT: D 537 MET cc_start: 0.7312 (mmt) cc_final: 0.7004 (mtt) REVERT: D 539 ASN cc_start: 0.7201 (t0) cc_final: 0.6996 (t160) REVERT: E 41 GLU cc_start: 0.6847 (tp30) cc_final: 0.6584 (tp30) REVERT: E 68 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8017 (ttm110) REVERT: E 83 LYS cc_start: 0.8839 (mttt) cc_final: 0.8314 (mtpp) REVERT: E 152 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8102 (mmtm) REVERT: E 173 ASP cc_start: 0.7970 (p0) cc_final: 0.7680 (p0) REVERT: E 177 LYS cc_start: 0.7585 (tptm) cc_final: 0.7200 (ttpp) REVERT: E 288 GLN cc_start: 0.6495 (mt0) cc_final: 0.6164 (tm-30) REVERT: E 355 ASP cc_start: 0.8183 (m-30) cc_final: 0.7857 (m-30) REVERT: E 356 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7536 (mt0) REVERT: E 362 ARG cc_start: 0.7505 (mtm110) cc_final: 0.7171 (mtt90) REVERT: E 375 MET cc_start: 0.9089 (mtp) cc_final: 0.8768 (mtp) REVERT: E 404 LYS cc_start: 0.8604 (tttt) cc_final: 0.8272 (ttmm) REVERT: E 444 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7052 (tm-30) REVERT: E 453 PHE cc_start: 0.7314 (m-80) cc_final: 0.7020 (m-80) REVERT: E 472 GLN cc_start: 0.8327 (mt0) cc_final: 0.7788 (mt0) REVERT: F 26 ILE cc_start: 0.7243 (tt) cc_final: 0.6765 (pp) REVERT: F 70 ILE cc_start: 0.7465 (mm) cc_final: 0.6784 (tt) REVERT: G 11 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5384 (pp20) REVERT: G 37 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6643 (tm-30) REVERT: G 63 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7611 (tttt) REVERT: G 83 LYS cc_start: 0.6146 (tttt) cc_final: 0.5864 (ttpt) REVERT: G 115 ASP cc_start: 0.7824 (m-30) cc_final: 0.7315 (t70) REVERT: G 154 LYS cc_start: 0.8752 (mtpm) cc_final: 0.8464 (mttp) REVERT: G 179 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: G 181 ASP cc_start: 0.6180 (p0) cc_final: 0.5895 (m-30) REVERT: G 182 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5742 (tm-30) outliers start: 89 outliers final: 12 residues processed: 547 average time/residue: 0.7876 time to fit residues: 484.6207 Evaluate side-chains 328 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 307 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 414 ARG Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 403 PRO Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 179 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 296 ASN B 51 HIS B 542 ASN C 48 GLN C 272 GLN C 460 GLN C 505 ASN C 513 GLN D 193 ASN D 250 HIS D 347 ASN D 427 HIS A D 468 GLN D 513 GLN E 13 ASN E 24 ASN E 116 ASN E 125 GLN E 535 ASN F 57 HIS F 164 GLN G 39 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109777 restraints weight = 57473.102| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.74 r_work: 0.2894 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25999 Z= 0.134 Angle : 0.568 11.709 35641 Z= 0.302 Chirality : 0.040 0.174 3984 Planarity : 0.004 0.042 4197 Dihedral : 16.567 102.132 4610 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.97 % Rotamer: Outliers : 2.82 % Allowed : 12.65 % Favored : 84.53 % 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: 1.84 (0.16), residues: 2822 helix: 2.38 (0.14), residues: 1352 sheet: 0.07 (0.25), residues: 430 loop : 0.25 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 160 TYR 0.017 0.001 TYR B 104 PHE 0.014 0.001 PHE G 180 TRP 0.023 0.002 TRP C 245 HIS 0.005 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00276 (25991) covalent geometry : angle 0.56490 (35629) hydrogen bonds : bond 0.04616 ( 1295) hydrogen bonds : angle 4.24778 ( 3574) metal coordination : bond 0.00748 ( 8) metal coordination : angle 3.17305 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 327 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8585 (mmm) cc_final: 0.8376 (mmm) REVERT: A 219 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8208 (mtt180) REVERT: A 304 MET cc_start: 0.8316 (mmm) cc_final: 0.8081 (mmm) REVERT: A 305 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 94 ASN cc_start: 0.8778 (m-40) cc_final: 0.8514 (m-40) REVERT: B 119 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8472 (ttmt) REVERT: B 170 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: B 224 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7678 (pt0) REVERT: B 404 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8258 (tptp) REVERT: B 465 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8098 (tm-30) REVERT: C 42 MET cc_start: 0.8080 (mtp) cc_final: 0.7772 (ttm) REVERT: C 46 TYR cc_start: 0.8626 (t80) cc_final: 0.8164 (t80) REVERT: C 152 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8086 (mptt) REVERT: C 311 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: C 336 MET cc_start: 0.7835 (tpp) cc_final: 0.6775 (mpt) REVERT: C 348 ASP cc_start: 0.7785 (m-30) cc_final: 0.7513 (m-30) REVERT: C 436 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8198 (mt-10) REVERT: C 454 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8794 (mp) REVERT: C 465 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: C 523 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8235 (pt) REVERT: C 526 LYS cc_start: 0.8060 (mttp) cc_final: 0.7798 (mtpp) REVERT: D 320 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8059 (mmtt) REVERT: D 396 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8081 (tt0) REVERT: D 450 ASP cc_start: 0.8136 (t70) cc_final: 0.7468 (t0) REVERT: D 455 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7639 (p0) REVERT: E 41 GLU cc_start: 0.7619 (tp30) cc_final: 0.7332 (tp30) REVERT: E 68 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.8176 (ttm110) REVERT: E 83 LYS cc_start: 0.8869 (mttt) cc_final: 0.8493 (mtpp) REVERT: E 152 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8075 (mmtm) REVERT: E 173 ASP cc_start: 0.7912 (p0) cc_final: 0.7595 (p0) REVERT: E 177 LYS cc_start: 0.7897 (tptm) cc_final: 0.7626 (ttpp) REVERT: E 293 LEU cc_start: 0.7005 (tp) cc_final: 0.6801 (tm) REVERT: E 320 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8322 (ttpp) REVERT: E 355 ASP cc_start: 0.8329 (m-30) cc_final: 0.8011 (m-30) REVERT: E 356 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7854 (mt0) REVERT: E 375 MET cc_start: 0.9099 (mtp) cc_final: 0.8757 (mtp) REVERT: E 453 PHE cc_start: 0.7593 (m-80) cc_final: 0.7299 (m-80) REVERT: E 472 GLN cc_start: 0.8543 (mt0) cc_final: 0.8272 (mt0) REVERT: E 499 ASN cc_start: 0.6155 (t0) cc_final: 0.5857 (t160) REVERT: G 38 MET cc_start: 0.6859 (ttp) cc_final: 0.6621 (ttp) REVERT: G 63 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7783 (tttt) REVERT: G 115 ASP cc_start: 0.7919 (m-30) cc_final: 0.7276 (t70) REVERT: G 164 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: G 172 TYR cc_start: 0.8147 (t80) cc_final: 0.7915 (t80) REVERT: G 177 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6290 (pp) REVERT: G 181 ASP cc_start: 0.6263 (p0) cc_final: 0.5932 (m-30) REVERT: G 182 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6147 (tm-30) REVERT: G 186 ASN cc_start: 0.7072 (m-40) cc_final: 0.6513 (m110) outliers start: 70 outliers final: 13 residues processed: 368 average time/residue: 0.8005 time to fit residues: 331.0655 Evaluate side-chains 305 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN B 51 HIS B 427 HIS ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN E 24 ASN E 94 ASN E 427 HIS F 57 HIS G 148 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105071 restraints weight = 73012.830| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.21 r_work: 0.2826 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25999 Z= 0.153 Angle : 0.566 11.299 35641 Z= 0.297 Chirality : 0.041 0.205 3984 Planarity : 0.004 0.046 4197 Dihedral : 16.316 95.386 4564 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.58 % Allowed : 14.24 % Favored : 83.18 % 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: 1.78 (0.16), residues: 2822 helix: 2.37 (0.14), residues: 1353 sheet: 0.06 (0.25), residues: 448 loop : 0.16 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 2 TYR 0.015 0.002 TYR C 104 PHE 0.015 0.002 PHE G 180 TRP 0.019 0.002 TRP C 245 HIS 0.007 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00352 (25991) covalent geometry : angle 0.56445 (35629) hydrogen bonds : bond 0.04669 ( 1295) hydrogen bonds : angle 4.12850 ( 3574) metal coordination : bond 0.00840 ( 8) metal coordination : angle 2.44081 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 304 MET cc_start: 0.8394 (mmm) cc_final: 0.8119 (mmm) REVERT: A 305 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: B 119 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8384 (ttmt) REVERT: B 170 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: B 224 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7750 (pt0) REVERT: B 375 MET cc_start: 0.9245 (mtp) cc_final: 0.8972 (mtp) REVERT: B 404 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8366 (tptp) REVERT: B 465 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8215 (tm-30) REVERT: B 530 SER cc_start: 0.8238 (t) cc_final: 0.7838 (m) REVERT: C 42 MET cc_start: 0.8070 (mtp) cc_final: 0.7769 (ttm) REVERT: C 46 TYR cc_start: 0.8682 (t80) cc_final: 0.8186 (t80) REVERT: C 152 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8118 (mptt) REVERT: C 221 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7142 (mtm-85) REVERT: C 311 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: C 336 MET cc_start: 0.7897 (tpp) cc_final: 0.6739 (mpt) REVERT: C 436 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8233 (mt-10) REVERT: C 454 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 474 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: C 526 LYS cc_start: 0.8087 (mttp) cc_final: 0.7786 (mtpp) REVERT: D 41 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: D 320 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8076 (mmtt) REVERT: D 396 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8087 (tt0) REVERT: D 455 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7602 (p0) REVERT: D 474 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8520 (mtp) REVERT: D 539 ASN cc_start: 0.7835 (t0) cc_final: 0.7579 (m-40) REVERT: E 41 GLU cc_start: 0.7748 (tp30) cc_final: 0.7426 (tp30) REVERT: E 68 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8092 (ttm110) REVERT: E 83 LYS cc_start: 0.8890 (mttt) cc_final: 0.8483 (mtpp) REVERT: E 177 LYS cc_start: 0.8089 (tptm) cc_final: 0.7757 (ttpp) REVERT: E 293 LEU cc_start: 0.6859 (tp) cc_final: 0.6608 (tm) REVERT: E 375 MET cc_start: 0.9108 (mtp) cc_final: 0.8794 (mtp) REVERT: E 472 GLN cc_start: 0.8758 (mt0) cc_final: 0.8464 (mt0) REVERT: E 499 ASN cc_start: 0.6095 (t0) cc_final: 0.5856 (t160) REVERT: E 539 ASN cc_start: 0.6635 (m-40) cc_final: 0.6434 (m110) REVERT: F 52 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7645 (mtm180) REVERT: F 139 LYS cc_start: 0.7676 (tttt) cc_final: 0.7453 (ttmt) REVERT: F 190 ARG cc_start: 0.7786 (ptt180) cc_final: 0.7259 (mtp180) REVERT: G 63 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7702 (tttt) REVERT: G 164 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: G 172 TYR cc_start: 0.8148 (t80) cc_final: 0.7831 (t80) REVERT: G 177 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6332 (pp) REVERT: G 181 ASP cc_start: 0.6231 (p0) cc_final: 0.5880 (m-30) REVERT: G 182 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6143 (tm-30) REVERT: G 186 ASN cc_start: 0.7044 (m-40) cc_final: 0.6529 (m110) REVERT: G 188 MET cc_start: 0.7239 (mmm) cc_final: 0.7038 (mmm) outliers start: 64 outliers final: 23 residues processed: 323 average time/residue: 0.8465 time to fit residues: 307.3673 Evaluate side-chains 310 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 68 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS C 48 GLN E 24 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107390 restraints weight = 64335.451| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.94 r_work: 0.2879 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25999 Z= 0.124 Angle : 0.517 10.373 35641 Z= 0.271 Chirality : 0.039 0.156 3984 Planarity : 0.003 0.050 4197 Dihedral : 16.115 95.716 4564 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.97 % Rotamer: Outliers : 2.54 % Allowed : 14.88 % Favored : 82.59 % 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: 1.85 (0.16), residues: 2822 helix: 2.47 (0.14), residues: 1353 sheet: 0.04 (0.25), residues: 448 loop : 0.15 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 160 TYR 0.017 0.001 TYR B 104 PHE 0.012 0.001 PHE B 226 TRP 0.017 0.001 TRP C 245 HIS 0.006 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00280 (25991) covalent geometry : angle 0.51558 (35629) hydrogen bonds : bond 0.03984 ( 1295) hydrogen bonds : angle 3.95825 ( 3574) metal coordination : bond 0.00800 ( 8) metal coordination : angle 2.28708 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 219 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8273 (mtt180) REVERT: A 304 MET cc_start: 0.8440 (mmm) cc_final: 0.8168 (mmm) REVERT: A 305 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: B 119 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8299 (ttmt) REVERT: B 170 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: B 224 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7683 (pt0) REVERT: B 375 MET cc_start: 0.9247 (mtp) cc_final: 0.8990 (mtp) REVERT: B 404 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8290 (tptp) REVERT: B 472 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: B 530 SER cc_start: 0.8155 (t) cc_final: 0.7805 (m) REVERT: C 42 MET cc_start: 0.7940 (mtp) cc_final: 0.7683 (ttm) REVERT: C 46 TYR cc_start: 0.8675 (t80) cc_final: 0.8202 (t80) REVERT: C 152 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8070 (mptt) REVERT: C 221 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7012 (mtm-85) REVERT: C 279 MET cc_start: 0.1633 (mmp) cc_final: 0.0671 (tpt) REVERT: C 311 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: C 336 MET cc_start: 0.7804 (tpp) cc_final: 0.6652 (mpt) REVERT: C 436 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8142 (mt-10) REVERT: C 474 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8273 (mtt) REVERT: C 500 SER cc_start: 0.7651 (m) cc_final: 0.7308 (t) REVERT: C 523 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8467 (pt) REVERT: C 526 LYS cc_start: 0.8098 (mttp) cc_final: 0.7777 (mtpp) REVERT: D 41 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: D 138 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: D 320 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8025 (mmtt) REVERT: D 396 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8071 (tt0) REVERT: D 450 ASP cc_start: 0.8222 (t0) cc_final: 0.7780 (t0) REVERT: D 455 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7578 (p0) REVERT: D 539 ASN cc_start: 0.8008 (t0) cc_final: 0.7731 (m-40) REVERT: E 41 GLU cc_start: 0.7734 (tp30) cc_final: 0.7488 (tp30) REVERT: E 42 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7748 (ttp) REVERT: E 68 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7957 (ttm110) REVERT: E 83 LYS cc_start: 0.8874 (mttt) cc_final: 0.8432 (mtpp) REVERT: E 293 LEU cc_start: 0.7082 (tp) cc_final: 0.6809 (tm) REVERT: E 375 MET cc_start: 0.9110 (mtp) cc_final: 0.8718 (mtp) REVERT: E 472 GLN cc_start: 0.8781 (mt0) cc_final: 0.8495 (mt0) REVERT: F 52 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7736 (mtm180) REVERT: F 190 ARG cc_start: 0.7853 (ptt180) cc_final: 0.7395 (mtp180) REVERT: G 63 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7780 (tttt) REVERT: G 142 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7154 (tp30) REVERT: G 164 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8006 (mm110) REVERT: G 172 TYR cc_start: 0.8131 (t80) cc_final: 0.7885 (t80) REVERT: G 181 ASP cc_start: 0.6156 (p0) cc_final: 0.5773 (m-30) REVERT: G 182 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6353 (tm-30) REVERT: G 186 ASN cc_start: 0.7261 (m-40) cc_final: 0.6868 (m110) outliers start: 63 outliers final: 20 residues processed: 329 average time/residue: 0.7960 time to fit residues: 293.8157 Evaluate side-chains 297 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 41 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 200 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 225 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS C 508 GLN D 125 GLN E 24 ASN E 539 ASN G 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109747 restraints weight = 73832.634| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.36 r_work: 0.2856 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25999 Z= 0.109 Angle : 0.501 9.350 35641 Z= 0.262 Chirality : 0.038 0.159 3984 Planarity : 0.003 0.051 4197 Dihedral : 15.974 93.934 4564 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % Rotamer: Outliers : 2.22 % Allowed : 15.51 % Favored : 82.27 % 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: 1.97 (0.16), residues: 2822 helix: 2.59 (0.14), residues: 1355 sheet: -0.00 (0.25), residues: 448 loop : 0.22 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 533 TYR 0.017 0.001 TYR B 104 PHE 0.010 0.001 PHE B 242 TRP 0.016 0.001 TRP C 245 HIS 0.007 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00238 (25991) covalent geometry : angle 0.49937 (35629) hydrogen bonds : bond 0.03619 ( 1295) hydrogen bonds : angle 3.85000 ( 3574) metal coordination : bond 0.00676 ( 8) metal coordination : angle 2.07985 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8283 (mtt180) REVERT: A 304 MET cc_start: 0.8407 (mmm) cc_final: 0.8124 (mmm) REVERT: A 305 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: B 119 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8311 (ttmm) REVERT: B 170 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 224 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7706 (pt0) REVERT: B 375 MET cc_start: 0.9230 (mtp) cc_final: 0.8921 (mtp) REVERT: B 404 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8323 (tptp) REVERT: B 472 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: B 530 SER cc_start: 0.8214 (t) cc_final: 0.7847 (m) REVERT: C 42 MET cc_start: 0.8005 (mtp) cc_final: 0.7761 (ttm) REVERT: C 46 TYR cc_start: 0.8728 (t80) cc_final: 0.8293 (t80) REVERT: C 120 GLU cc_start: 0.7926 (tt0) cc_final: 0.7686 (tt0) REVERT: C 152 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8171 (mptt) REVERT: C 221 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7161 (mtm-85) REVERT: C 320 LYS cc_start: 0.8346 (mttp) cc_final: 0.8114 (ttmt) REVERT: C 336 MET cc_start: 0.7818 (tpp) cc_final: 0.6645 (mpt) REVERT: C 436 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8211 (mt-10) REVERT: C 474 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8220 (mtt) REVERT: C 500 SER cc_start: 0.7666 (m) cc_final: 0.7103 (t) REVERT: C 523 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8562 (pp) REVERT: C 526 LYS cc_start: 0.8146 (mttp) cc_final: 0.7819 (mtpp) REVERT: D 41 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: D 138 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: D 320 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8062 (mmtt) REVERT: D 396 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8121 (tt0) REVERT: D 450 ASP cc_start: 0.8261 (t0) cc_final: 0.7759 (t0) REVERT: D 455 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7566 (p0) REVERT: D 474 MET cc_start: 0.8924 (mtm) cc_final: 0.8595 (mtp) REVERT: D 539 ASN cc_start: 0.7994 (t0) cc_final: 0.7709 (m-40) REVERT: E 13 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7746 (t0) REVERT: E 41 GLU cc_start: 0.7798 (tp30) cc_final: 0.7521 (tp30) REVERT: E 42 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7810 (ttp) REVERT: E 83 LYS cc_start: 0.8915 (mttt) cc_final: 0.8451 (mtpp) REVERT: E 293 LEU cc_start: 0.6927 (tp) cc_final: 0.6659 (tm) REVERT: E 375 MET cc_start: 0.9096 (mtp) cc_final: 0.8729 (mtp) REVERT: E 472 GLN cc_start: 0.8825 (mt0) cc_final: 0.8539 (mt0) REVERT: F 52 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7780 (mtm180) REVERT: F 190 ARG cc_start: 0.7811 (ptt180) cc_final: 0.7288 (mtp180) REVERT: G 63 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7747 (tttt) REVERT: G 64 PHE cc_start: 0.7274 (m-80) cc_final: 0.7049 (m-80) REVERT: G 142 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7164 (tp30) REVERT: G 164 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8061 (mm110) REVERT: G 172 TYR cc_start: 0.8130 (t80) cc_final: 0.7905 (t80) REVERT: G 181 ASP cc_start: 0.5927 (p0) cc_final: 0.5704 (m-30) REVERT: G 182 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6120 (tm-30) REVERT: G 186 ASN cc_start: 0.7132 (m-40) cc_final: 0.6636 (m110) outliers start: 55 outliers final: 17 residues processed: 317 average time/residue: 0.8241 time to fit residues: 293.1691 Evaluate side-chains 298 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 150 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 257 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 231 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 51 HIS B 94 ASN B 466 ASN E 24 ASN E 451 GLN E 539 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112740 restraints weight = 57754.311| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.36 r_work: 0.2873 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25999 Z= 0.115 Angle : 0.501 9.005 35641 Z= 0.262 Chirality : 0.038 0.154 3984 Planarity : 0.003 0.050 4197 Dihedral : 15.978 93.746 4564 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.18 % Favored : 98.79 % Rotamer: Outliers : 2.26 % Allowed : 15.79 % Favored : 81.95 % 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: 1.96 (0.16), residues: 2822 helix: 2.59 (0.14), residues: 1357 sheet: -0.03 (0.25), residues: 448 loop : 0.22 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.022 0.001 TYR C 104 PHE 0.012 0.001 PHE B 242 TRP 0.015 0.001 TRP C 245 HIS 0.007 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00257 (25991) covalent geometry : angle 0.49939 (35629) hydrogen bonds : bond 0.03708 ( 1295) hydrogen bonds : angle 3.83740 ( 3574) metal coordination : bond 0.00691 ( 8) metal coordination : angle 1.88916 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8583 (mtt-85) cc_final: 0.8236 (mtt180) REVERT: A 271 ASN cc_start: 0.8745 (m-40) cc_final: 0.8526 (m-40) REVERT: A 304 MET cc_start: 0.8408 (mmm) cc_final: 0.8167 (mmm) REVERT: A 305 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 119 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8275 (ttmm) REVERT: B 170 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: B 191 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: B 224 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7628 (pt0) REVERT: B 375 MET cc_start: 0.9273 (mtp) cc_final: 0.9020 (mtp) REVERT: B 404 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8275 (tptp) REVERT: B 472 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: C 42 MET cc_start: 0.7941 (mtp) cc_final: 0.7736 (ttm) REVERT: C 46 TYR cc_start: 0.8695 (t80) cc_final: 0.8215 (t80) REVERT: C 120 GLU cc_start: 0.7859 (tt0) cc_final: 0.7631 (tt0) REVERT: C 126 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7718 (ptm160) REVERT: C 152 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7999 (mptt) REVERT: C 336 MET cc_start: 0.7763 (tpp) cc_final: 0.6571 (mpt) REVERT: C 436 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8122 (mt-10) REVERT: C 474 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8208 (mtt) REVERT: C 500 SER cc_start: 0.7473 (m) cc_final: 0.7077 (t) REVERT: C 523 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8534 (pp) REVERT: C 526 LYS cc_start: 0.8119 (mttp) cc_final: 0.7756 (mtpp) REVERT: D 138 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: D 320 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7964 (mmtt) REVERT: D 396 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8075 (tt0) REVERT: D 450 ASP cc_start: 0.8209 (t0) cc_final: 0.7640 (t0) REVERT: D 455 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7544 (p0) REVERT: D 474 MET cc_start: 0.8931 (mtm) cc_final: 0.8592 (mtp) REVERT: D 539 ASN cc_start: 0.7904 (t0) cc_final: 0.7649 (m-40) REVERT: E 13 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7721 (t0) REVERT: E 41 GLU cc_start: 0.7753 (tp30) cc_final: 0.7509 (tp30) REVERT: E 42 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7767 (ttp) REVERT: E 83 LYS cc_start: 0.8854 (mttt) cc_final: 0.8399 (mtpp) REVERT: E 298 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5163 (mp0) REVERT: E 375 MET cc_start: 0.9121 (mtp) cc_final: 0.8740 (mtp) REVERT: E 472 GLN cc_start: 0.8799 (mt0) cc_final: 0.8502 (mt0) REVERT: F 52 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7754 (mtm180) REVERT: F 95 ASP cc_start: 0.7968 (m-30) cc_final: 0.7649 (m-30) REVERT: F 190 ARG cc_start: 0.7808 (ptt180) cc_final: 0.7292 (mtp180) REVERT: G 37 GLU cc_start: 0.6393 (pp20) cc_final: 0.6051 (pt0) REVERT: G 63 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7715 (tttt) REVERT: G 164 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7961 (mm110) REVERT: G 172 TYR cc_start: 0.8094 (t80) cc_final: 0.7848 (t80) REVERT: G 181 ASP cc_start: 0.5730 (p0) cc_final: 0.5517 (m-30) REVERT: G 182 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6250 (tm-30) REVERT: G 186 ASN cc_start: 0.7378 (m-40) cc_final: 0.6988 (m110) outliers start: 55 outliers final: 20 residues processed: 310 average time/residue: 0.8653 time to fit residues: 301.5517 Evaluate side-chains 297 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS E 24 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 GLN E 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112626 restraints weight = 64055.522| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.93 r_work: 0.2822 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25999 Z= 0.126 Angle : 0.517 10.134 35641 Z= 0.270 Chirality : 0.039 0.264 3984 Planarity : 0.003 0.050 4197 Dihedral : 15.975 94.311 4562 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.86 % Rotamer: Outliers : 2.14 % Allowed : 16.07 % Favored : 81.79 % 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: 1.92 (0.16), residues: 2822 helix: 2.56 (0.14), residues: 1357 sheet: -0.04 (0.25), residues: 448 loop : 0.19 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.018 0.001 TYR C 104 PHE 0.013 0.001 PHE B 242 TRP 0.015 0.001 TRP C 245 HIS 0.007 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00286 (25991) covalent geometry : angle 0.51642 (35629) hydrogen bonds : bond 0.03851 ( 1295) hydrogen bonds : angle 3.88277 ( 3574) metal coordination : bond 0.00710 ( 8) metal coordination : angle 1.85379 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.8198 (mtt180) REVERT: A 304 MET cc_start: 0.8310 (mmm) cc_final: 0.8045 (mmm) REVERT: A 305 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: B 119 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8310 (ttmm) REVERT: B 170 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: B 191 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: B 224 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7610 (pt0) REVERT: B 375 MET cc_start: 0.9318 (mtp) cc_final: 0.9063 (mtp) REVERT: B 404 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8269 (tptp) REVERT: B 472 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: C 42 MET cc_start: 0.7869 (mtp) cc_final: 0.7591 (ttm) REVERT: C 46 TYR cc_start: 0.8686 (t80) cc_final: 0.8244 (t80) REVERT: C 120 GLU cc_start: 0.7949 (tt0) cc_final: 0.7683 (tt0) REVERT: C 126 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7620 (ptm160) REVERT: C 152 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8129 (mptt) REVERT: C 221 ARG cc_start: 0.7953 (mtp85) cc_final: 0.6977 (mtm-85) REVERT: C 336 MET cc_start: 0.7708 (tpp) cc_final: 0.6516 (mpt) REVERT: C 436 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 474 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: C 500 SER cc_start: 0.7650 (m) cc_final: 0.7287 (t) REVERT: C 523 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 526 LYS cc_start: 0.8119 (mttp) cc_final: 0.7733 (mtpp) REVERT: D 41 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: D 320 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7872 (mmtt) REVERT: D 396 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8099 (tt0) REVERT: D 450 ASP cc_start: 0.8192 (t0) cc_final: 0.7645 (t0) REVERT: D 455 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7532 (p0) REVERT: D 474 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8632 (mtp) REVERT: E 13 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7706 (t0) REVERT: E 41 GLU cc_start: 0.7652 (tp30) cc_final: 0.7397 (tp30) REVERT: E 42 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: E 83 LYS cc_start: 0.8892 (mttt) cc_final: 0.8374 (mtpp) REVERT: E 293 LEU cc_start: 0.6794 (tp) cc_final: 0.6560 (tm) REVERT: E 298 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.5081 (mp0) REVERT: E 375 MET cc_start: 0.9149 (mtp) cc_final: 0.8779 (mtp) REVERT: F 52 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7780 (mtm180) REVERT: F 95 ASP cc_start: 0.7958 (m-30) cc_final: 0.7641 (m-30) REVERT: F 138 LYS cc_start: 0.7982 (tppp) cc_final: 0.7683 (tptp) REVERT: F 190 ARG cc_start: 0.7827 (ptt180) cc_final: 0.7271 (mtp180) REVERT: G 63 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7639 (tttt) REVERT: G 64 PHE cc_start: 0.7296 (m-80) cc_final: 0.7044 (m-10) REVERT: G 142 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7138 (tp30) REVERT: G 164 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7928 (mm110) REVERT: G 172 TYR cc_start: 0.7959 (t80) cc_final: 0.7718 (t80) outliers start: 52 outliers final: 22 residues processed: 297 average time/residue: 0.8069 time to fit residues: 268.3534 Evaluate side-chains 294 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 70 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 51 HIS D 94 ASN E 24 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112446 restraints weight = 69493.632| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.35 r_work: 0.2784 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25999 Z= 0.120 Angle : 0.510 11.403 35641 Z= 0.267 Chirality : 0.039 0.287 3984 Planarity : 0.003 0.050 4197 Dihedral : 15.922 94.624 4562 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.61 % Rotamer: Outliers : 2.06 % Allowed : 16.34 % Favored : 81.59 % 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: 1.90 (0.16), residues: 2822 helix: 2.55 (0.14), residues: 1357 sheet: -0.10 (0.25), residues: 438 loop : 0.20 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 533 TYR 0.017 0.001 TYR C 104 PHE 0.013 0.001 PHE C 453 TRP 0.015 0.001 TRP C 245 HIS 0.008 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00270 (25991) covalent geometry : angle 0.50950 (35629) hydrogen bonds : bond 0.03770 ( 1295) hydrogen bonds : angle 3.86204 ( 3574) metal coordination : bond 0.00699 ( 8) metal coordination : angle 1.74030 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8296 (mtt180) REVERT: A 304 MET cc_start: 0.8416 (mmm) cc_final: 0.8166 (mmm) REVERT: A 305 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 119 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8369 (ttmm) REVERT: B 170 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: B 191 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: B 224 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7775 (pt0) REVERT: B 375 MET cc_start: 0.9291 (mtp) cc_final: 0.9041 (mtp) REVERT: B 404 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8367 (tptp) REVERT: C 42 MET cc_start: 0.8027 (mtp) cc_final: 0.7756 (ttm) REVERT: C 46 TYR cc_start: 0.8744 (t80) cc_final: 0.8349 (t80) REVERT: C 126 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7736 (ptm160) REVERT: C 152 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8149 (mptt) REVERT: C 221 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7236 (mtm-85) REVERT: C 336 MET cc_start: 0.7788 (tpp) cc_final: 0.6607 (mpt) REVERT: C 436 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 474 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: C 500 SER cc_start: 0.7692 (m) cc_final: 0.7406 (t) REVERT: C 523 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8598 (pp) REVERT: C 526 LYS cc_start: 0.8265 (mttp) cc_final: 0.7893 (mtpp) REVERT: D 320 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8043 (mmtt) REVERT: D 396 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8232 (tt0) REVERT: D 450 ASP cc_start: 0.8286 (t0) cc_final: 0.7754 (t0) REVERT: D 455 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7693 (p0) REVERT: D 474 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8652 (mtp) REVERT: E 41 GLU cc_start: 0.7798 (tp30) cc_final: 0.7526 (tp30) REVERT: E 42 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7844 (ttp) REVERT: E 83 LYS cc_start: 0.8949 (mttt) cc_final: 0.8483 (mtpp) REVERT: E 298 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.5156 (mp0) REVERT: E 375 MET cc_start: 0.9147 (mtp) cc_final: 0.8796 (mtp) REVERT: F 95 ASP cc_start: 0.7976 (m-30) cc_final: 0.7679 (m-30) REVERT: F 138 LYS cc_start: 0.8057 (tppp) cc_final: 0.7768 (tptp) REVERT: F 190 ARG cc_start: 0.7840 (ptt180) cc_final: 0.7251 (mtp180) REVERT: G 63 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7592 (tttt) REVERT: G 64 PHE cc_start: 0.7302 (m-80) cc_final: 0.7057 (m-10) REVERT: G 142 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7331 (tp30) REVERT: G 164 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8123 (mm110) REVERT: G 172 TYR cc_start: 0.8013 (t80) cc_final: 0.7775 (t80) outliers start: 50 outliers final: 27 residues processed: 286 average time/residue: 0.8655 time to fit residues: 277.2001 Evaluate side-chains 286 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 282 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 51 HIS B 472 GLN D 94 ASN E 24 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109918 restraints weight = 67289.164| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.14 r_work: 0.2803 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25999 Z= 0.135 Angle : 0.527 11.176 35641 Z= 0.275 Chirality : 0.039 0.301 3984 Planarity : 0.004 0.049 4197 Dihedral : 15.998 95.438 4562 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Rotamer: Outliers : 1.90 % Allowed : 16.74 % Favored : 81.36 % 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: 1.80 (0.16), residues: 2822 helix: 2.45 (0.14), residues: 1364 sheet: -0.09 (0.24), residues: 448 loop : 0.13 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 221 TYR 0.017 0.001 TYR C 104 PHE 0.014 0.001 PHE B 242 TRP 0.014 0.001 TRP C 245 HIS 0.008 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00313 (25991) covalent geometry : angle 0.52607 (35629) hydrogen bonds : bond 0.04028 ( 1295) hydrogen bonds : angle 3.89446 ( 3574) metal coordination : bond 0.00738 ( 8) metal coordination : angle 1.70563 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8280 (mtt180) REVERT: A 304 MET cc_start: 0.8487 (mmm) cc_final: 0.8242 (mmm) REVERT: A 305 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 119 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8338 (ttmm) REVERT: B 170 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: B 191 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: B 224 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7739 (pt0) REVERT: B 375 MET cc_start: 0.9309 (mtp) cc_final: 0.9040 (mtp) REVERT: B 404 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8350 (tptp) REVERT: C 42 MET cc_start: 0.7958 (mtp) cc_final: 0.7730 (ttm) REVERT: C 46 TYR cc_start: 0.8725 (t80) cc_final: 0.8332 (t80) REVERT: C 152 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8020 (mptt) REVERT: C 221 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7204 (mtm-85) REVERT: C 336 MET cc_start: 0.7780 (tpp) cc_final: 0.6573 (mpt) REVERT: C 436 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 474 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: C 500 SER cc_start: 0.7714 (m) cc_final: 0.7493 (t) REVERT: C 523 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8587 (pp) REVERT: C 526 LYS cc_start: 0.8209 (mttp) cc_final: 0.7840 (mtpp) REVERT: D 130 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7811 (mpt) REVERT: D 320 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8000 (mmtt) REVERT: D 396 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8125 (tt0) REVERT: D 450 ASP cc_start: 0.8295 (t0) cc_final: 0.7803 (t0) REVERT: D 455 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7605 (p0) REVERT: D 474 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8642 (mtp) REVERT: E 41 GLU cc_start: 0.7715 (tp30) cc_final: 0.7501 (tp30) REVERT: E 42 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7833 (ttp) REVERT: E 83 LYS cc_start: 0.8899 (mttt) cc_final: 0.8438 (mtpp) REVERT: E 298 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5209 (mp0) REVERT: E 375 MET cc_start: 0.9158 (mtp) cc_final: 0.8805 (mtp) REVERT: F 138 LYS cc_start: 0.8020 (tppp) cc_final: 0.7776 (tptp) REVERT: F 190 ARG cc_start: 0.7809 (ptt180) cc_final: 0.7283 (mtp180) REVERT: G 7 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5499 (pp) REVERT: G 37 GLU cc_start: 0.6352 (pp20) cc_final: 0.5850 (pt0) REVERT: G 63 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7611 (tttt) REVERT: G 64 PHE cc_start: 0.7349 (m-80) cc_final: 0.7124 (m-10) REVERT: G 142 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7324 (tp30) REVERT: G 164 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8051 (mm110) REVERT: G 172 TYR cc_start: 0.8004 (t80) cc_final: 0.7782 (t80) outliers start: 46 outliers final: 25 residues processed: 277 average time/residue: 0.8410 time to fit residues: 261.4714 Evaluate side-chains 285 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 148 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 51 HIS B 472 GLN D 51 HIS ** D 402 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 HIS B D 539 ASN E 24 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN E 539 ASN F 28 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102836 restraints weight = 59845.708| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.74 r_work: 0.2824 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25999 Z= 0.214 Angle : 0.602 10.411 35641 Z= 0.312 Chirality : 0.043 0.256 3984 Planarity : 0.004 0.048 4197 Dihedral : 16.263 96.402 4562 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.75 % Favored : 98.22 % Rotamer: Outliers : 1.90 % Allowed : 16.78 % Favored : 81.32 % 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: 1.50 (0.15), residues: 2822 helix: 2.19 (0.14), residues: 1362 sheet: -0.05 (0.25), residues: 432 loop : -0.10 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 533 TYR 0.018 0.002 TYR B 104 PHE 0.019 0.002 PHE B 242 TRP 0.015 0.002 TRP C 245 HIS 0.009 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00513 (25991) covalent geometry : angle 0.60063 (35629) hydrogen bonds : bond 0.05124 ( 1295) hydrogen bonds : angle 4.12255 ( 3574) metal coordination : bond 0.00966 ( 8) metal coordination : angle 1.87179 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8645 (mtt-85) cc_final: 0.8310 (mtt180) REVERT: A 304 MET cc_start: 0.8568 (mmm) cc_final: 0.8328 (mmm) REVERT: B 119 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8345 (ttmm) REVERT: B 170 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: B 224 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7806 (pt0) REVERT: B 375 MET cc_start: 0.9255 (mtp) cc_final: 0.8977 (mtp) REVERT: B 404 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8449 (tptp) REVERT: C 46 TYR cc_start: 0.8726 (t80) cc_final: 0.8276 (t80) REVERT: C 126 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7783 (ptm160) REVERT: C 152 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: C 221 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7309 (mtm-85) REVERT: C 336 MET cc_start: 0.7910 (tpp) cc_final: 0.6684 (mpt) REVERT: C 436 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8184 (mt-10) REVERT: C 474 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8491 (mtt) REVERT: C 523 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8700 (pp) REVERT: C 526 LYS cc_start: 0.8148 (mttp) cc_final: 0.7799 (mtpp) REVERT: D 320 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8160 (mmtt) REVERT: D 396 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8117 (tt0) REVERT: D 450 ASP cc_start: 0.8288 (t0) cc_final: 0.7868 (t0) REVERT: D 455 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7690 (p0) REVERT: D 474 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8607 (mtp) REVERT: E 83 LYS cc_start: 0.8868 (mttt) cc_final: 0.8454 (mtpp) REVERT: E 298 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5167 (mp0) REVERT: E 375 MET cc_start: 0.9127 (mtp) cc_final: 0.8869 (mtp) REVERT: F 117 TYR cc_start: 0.8688 (m-80) cc_final: 0.8404 (m-80) REVERT: G 7 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5809 (pp) REVERT: G 37 GLU cc_start: 0.6225 (pp20) cc_final: 0.5857 (pt0) REVERT: G 64 PHE cc_start: 0.7410 (m-80) cc_final: 0.7204 (m-10) REVERT: G 142 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7405 (tp30) REVERT: G 164 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: G 172 TYR cc_start: 0.8065 (t80) cc_final: 0.7860 (t80) outliers start: 46 outliers final: 23 residues processed: 264 average time/residue: 0.8094 time to fit residues: 240.1091 Evaluate side-chains 264 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 133 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 51 HIS B 472 GLN D 94 ASN ** D 402 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 HIS B E 24 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110176 restraints weight = 62889.880| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.77 r_work: 0.2785 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25999 Z= 0.155 Angle : 0.552 11.568 35641 Z= 0.287 Chirality : 0.040 0.244 3984 Planarity : 0.004 0.048 4197 Dihedral : 16.125 97.183 4558 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Rotamer: Outliers : 1.59 % Allowed : 17.26 % Favored : 81.16 % 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: 1.50 (0.15), residues: 2822 helix: 2.19 (0.14), residues: 1376 sheet: -0.04 (0.25), residues: 432 loop : -0.14 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 533 TYR 0.017 0.002 TYR B 104 PHE 0.016 0.001 PHE B 242 TRP 0.013 0.001 TRP C 245 HIS 0.005 0.001 HIS B 400 Details of bonding type rmsd covalent geometry : bond 0.00363 (25991) covalent geometry : angle 0.55133 (35629) hydrogen bonds : bond 0.04355 ( 1295) hydrogen bonds : angle 4.01614 ( 3574) metal coordination : bond 0.00833 ( 8) metal coordination : angle 1.87035 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9988.46 seconds wall clock time: 170 minutes 35.29 seconds (10235.29 seconds total)