Starting phenix.real_space_refine on Mon Jul 6 20:02:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r72_24290/07_2026/7r72_24290.cif" } resolution = 3.07 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 700 5.49 5 S 79 5.16 5 C 22178 2.51 5 N 7150 2.21 5 O 9335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39443 Number of models: 1 Model: "" Number of chains: 25 Chain: "1" Number of atoms: 13716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 13716 Classifications: {'RNA': 641} Modifications used: {'rna2p_pur': 63, 'rna2p_pyr': 48, 'rna3p_pur': 290, 'rna3p_pyr': 240} Link IDs: {'rna2p': 111, 'rna3p': 529} Chain breaks: 12 Chain: "2" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1255 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 47} Chain breaks: 3 Chain: "8" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "G" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 175 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2675 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "P" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain breaks: 4 Chain: "R" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "X" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "b" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 431 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 593 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 2 Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 212 Classifications: {'peptide': 27} Link IDs: {'PCIS': 1, 'TRANS': 25} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "m" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3302 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 385} Chain breaks: 3 Chain: "n" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 861 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "p" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2629 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Chain: "t" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 221 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "u" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 481 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "w" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1562 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 6 Chain: "x" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4340 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24691 SG CYS g 44 98.529 84.835 124.691 1.00 16.44 S ATOM 24709 SG CYS g 47 96.450 82.797 122.332 1.00 18.06 S ATOM 24963 SG CYS g 81 94.739 85.362 124.581 1.00 15.15 S ATOM 24982 SG CYS g 84 96.016 82.289 126.142 1.00 14.24 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ILE m 445 " occ=0.74 ... (6 atoms not shown) pdb=" CD1 ILE m 445 " occ=0.74 residue: pdb=" N ILE m 466 " occ=0.64 ... (6 atoms not shown) pdb=" CD1 ILE m 466 " occ=0.64 residue: pdb=" N PRO m 484 " occ=0.79 ... (5 atoms not shown) pdb=" CD PRO m 484 " occ=0.79 residue: pdb=" N ASP m 485 " occ=0.85 ... (6 atoms not shown) pdb=" OD2 ASP m 485 " occ=0.85 residue: pdb=" N LYS m 529 " occ=0.59 ... (7 atoms not shown) pdb=" NZ LYS m 529 " occ=0.59 residue: pdb=" N ARG m 720 " occ=0.60 ... (9 atoms not shown) pdb=" NH2 ARG m 720 " occ=0.60 Time building chain proxies: 6.57, per 1000 atoms: 0.17 Number of scatterers: 39443 At special positions: 0 Unit cell: (180.36, 174.96, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 79 16.00 P 700 15.00 O 9335 8.00 N 7150 7.00 C 22178 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: 3.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " Number of angles added : 6 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 28 sheets defined 43.3% alpha, 15.8% beta 213 base pairs and 345 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain '8' and resid 5 through 15 Processing helix chain '8' and resid 15 through 35 removed outlier: 4.040A pdb=" N GLY 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 41 through 50 Processing helix chain '8' and resid 51 through 60 Processing helix chain 'G' and resid 47 through 52 removed outlier: 4.174A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'I' and resid 131 through 150 removed outlier: 4.246A pdb=" N GLU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 165 Processing helix chain 'I' and resid 170 through 189 removed outlier: 3.913A pdb=" N VAL I 182 " --> pdb=" O MET I 178 " (cutoff:3.500A) Proline residue: I 183 - end of helix Processing helix chain 'I' and resid 198 through 203 removed outlier: 4.128A pdb=" N LYS I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 236 removed outlier: 3.504A pdb=" N LYS I 236 " --> pdb=" O GLN I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 261 removed outlier: 3.890A pdb=" N SER I 261 " --> pdb=" O LYS I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.794A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 304 Processing helix chain 'I' and resid 308 through 325 removed outlier: 3.538A pdb=" N ILE I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 Processing helix chain 'I' and resid 336 through 344 removed outlier: 6.271A pdb=" N ASP I 341 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL I 342 " --> pdb=" O SER I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.679A pdb=" N ARG I 366 " --> pdb=" O LYS I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 421 removed outlier: 3.812A pdb=" N GLU I 400 " --> pdb=" O ALA I 396 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 437 Processing helix chain 'I' and resid 438 through 440 No H-bonds generated for 'chain 'I' and resid 438 through 440' Processing helix chain 'P' and resid 25 through 32 Processing helix chain 'P' and resid 84 through 90 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.803A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 162 removed outlier: 5.442A pdb=" N LYS R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA R 154 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 removed outlier: 3.816A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 Processing helix chain 'U' and resid 42 through 46 removed outlier: 3.770A pdb=" N GLY U 45 " --> pdb=" O LYS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 80 removed outlier: 3.790A pdb=" N ASN X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 131 through 138 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 99 through 102 Processing helix chain 'Z' and resid 103 through 124 Processing helix chain 'b' and resid 490 through 511 Processing helix chain 'b' and resid 527 through 539 removed outlier: 4.052A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 21 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'g' and resid 58 through 65 removed outlier: 3.787A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL g 65 " --> pdb=" O TYR g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'g' and resid 81 through 111 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 58 through 68 Processing helix chain 'm' and resid 393 through 397 Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'm' and resid 418 through 422 Processing helix chain 'm' and resid 519 through 532 removed outlier: 4.149A pdb=" N ASN m 525 " --> pdb=" O ASP m 521 " (cutoff:3.500A) Processing helix chain 'm' and resid 533 through 538 removed outlier: 3.655A pdb=" N THR m 538 " --> pdb=" O GLY m 535 " (cutoff:3.500A) Processing helix chain 'm' and resid 579 through 584 removed outlier: 3.548A pdb=" N GLU m 584 " --> pdb=" O GLN m 580 " (cutoff:3.500A) Processing helix chain 'm' and resid 616 through 619 removed outlier: 3.673A pdb=" N THR m 619 " --> pdb=" O SER m 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 616 through 619' Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 69 removed outlier: 3.629A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 551 through 556 Processing helix chain 'n' and resid 557 through 559 No H-bonds generated for 'chain 'n' and resid 557 through 559' Processing helix chain 'n' and resid 560 through 583 Processing helix chain 'p' and resid 237 through 241 removed outlier: 3.597A pdb=" N MET p 241 " --> pdb=" O TYR p 238 " (cutoff:3.500A) Processing helix chain 'p' and resid 245 through 252 removed outlier: 4.020A pdb=" N ASP p 249 " --> pdb=" O ASP p 245 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE p 250 " --> pdb=" O PRO p 246 " (cutoff:3.500A) Processing helix chain 'p' and resid 258 through 267 Processing helix chain 't' and resid 25 through 37 Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 105 through 112 Processing helix chain 'u' and resid 114 through 129 Processing helix chain 'u' and resid 130 through 138 Processing helix chain 'w' and resid 348 through 388 removed outlier: 4.097A pdb=" N ILE w 352 " --> pdb=" O GLU w 348 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN w 388 " --> pdb=" O ARG w 384 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 416 removed outlier: 3.814A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) Processing helix chain 'w' and resid 418 through 424 removed outlier: 3.896A pdb=" N LEU w 422 " --> pdb=" O ILE w 418 " (cutoff:3.500A) Processing helix chain 'w' and resid 455 through 479 removed outlier: 4.182A pdb=" N ALA w 459 " --> pdb=" O SER w 455 " (cutoff:3.500A) Processing helix chain 'w' and resid 481 through 490 removed outlier: 3.759A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG w 490 " --> pdb=" O ALA w 486 " (cutoff:3.500A) Processing helix chain 'w' and resid 552 through 560 Processing helix chain 'w' and resid 638 through 652 Processing helix chain 'w' and resid 696 through 701 Processing helix chain 'x' and resid 15 through 26 Processing helix chain 'x' and resid 31 through 42 removed outlier: 3.528A pdb=" N ILE x 38 " --> pdb=" O GLN x 34 " (cutoff:3.500A) Proline residue: x 39 - end of helix Processing helix chain 'x' and resid 56 through 72 Proline residue: x 64 - end of helix Processing helix chain 'x' and resid 92 through 108 Processing helix chain 'x' and resid 129 through 141 Processing helix chain 'x' and resid 148 through 158 Processing helix chain 'x' and resid 173 through 178 Processing helix chain 'x' and resid 182 through 193 removed outlier: 3.584A pdb=" N LYS x 188 " --> pdb=" O LYS x 184 " (cutoff:3.500A) Processing helix chain 'x' and resid 211 through 217 removed outlier: 3.700A pdb=" N PHE x 214 " --> pdb=" O SER x 211 " (cutoff:3.500A) Processing helix chain 'x' and resid 244 through 246 No H-bonds generated for 'chain 'x' and resid 244 through 246' Processing helix chain 'x' and resid 247 through 257 Processing helix chain 'x' and resid 270 through 287 Processing helix chain 'x' and resid 304 through 317 Processing helix chain 'x' and resid 353 through 358 Processing helix chain 'x' and resid 359 through 361 No H-bonds generated for 'chain 'x' and resid 359 through 361' Processing helix chain 'x' and resid 362 through 366 Processing helix chain 'x' and resid 378 through 389 removed outlier: 4.139A pdb=" N PHE x 382 " --> pdb=" O ARG x 378 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE x 383 " --> pdb=" O GLU x 379 " (cutoff:3.500A) Proline residue: x 384 - end of helix Processing helix chain 'x' and resid 406 through 416 Processing helix chain 'x' and resid 418 through 438 Processing helix chain 'x' and resid 451 through 459 Processing helix chain 'x' and resid 467 through 474 Processing helix chain 'x' and resid 502 through 515 removed outlier: 3.721A pdb=" N LYS x 507 " --> pdb=" O LYS x 503 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU x 508 " --> pdb=" O LYS x 504 " (cutoff:3.500A) Processing helix chain 'x' and resid 515 through 533 Processing helix chain 'x' and resid 536 through 558 removed outlier: 3.814A pdb=" N LYS x 556 " --> pdb=" O LYS x 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 127 through 128 Processing sheet with id=AA2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'U' and resid 54 through 58 removed outlier: 8.191A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AA5, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.826A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.642A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.971A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 12 through 15 Processing sheet with id=AA9, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.494A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 16 through 18 removed outlier: 3.616A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.390A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG k 46 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA k 23 " --> pdb=" O ASN k 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 399 through 405 Processing sheet with id=AB4, first strand: chain 'm' and resid 428 through 434 removed outlier: 5.215A pdb=" N CYS m 429 " --> pdb=" O THR m 806 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR m 806 " --> pdb=" O CYS m 429 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR m 431 " --> pdb=" O LEU m 804 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR m 801 " --> pdb=" O GLY m 797 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 440 through 445 removed outlier: 3.638A pdb=" N THR m 442 " --> pdb=" O GLY m 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR m 460 " --> pdb=" O SER m 456 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU m 465 " --> pdb=" O GLU m 471 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU m 471 " --> pdb=" O GLU m 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 488 through 493 removed outlier: 3.979A pdb=" N ILE m 589 " --> pdb=" O LEU m 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 599 through 602 Processing sheet with id=AB8, first strand: chain 'm' and resid 642 through 647 removed outlier: 5.943A pdb=" N VAL m 662 " --> pdb=" O LYS m 675 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS m 675 " --> pdb=" O VAL m 662 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE m 664 " --> pdb=" O VAL m 673 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 683 through 688 removed outlier: 6.584A pdb=" N SER m 698 " --> pdb=" O SER m 684 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE m 686 " --> pdb=" O ILE m 696 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE m 696 " --> pdb=" O ILE m 686 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE m 688 " --> pdb=" O ASN m 694 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN m 694 " --> pdb=" O ILE m 688 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 726 through 731 removed outlier: 3.515A pdb=" N SER m 728 " --> pdb=" O ALA m 741 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE m 747 " --> pdb=" O LYS m 769 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS m 769 " --> pdb=" O ILE m 747 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL m 749 " --> pdb=" O LEU m 767 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 96 through 100 removed outlier: 3.670A pdb=" N ASN p 98 " --> pdb=" O ILE p 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 106 through 110 removed outlier: 3.510A pdb=" N SER p 108 " --> pdb=" O GLY p 121 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL p 127 " --> pdb=" O GLN p 139 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN p 139 " --> pdb=" O VAL p 127 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR p 129 " --> pdb=" O GLN p 137 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN p 137 " --> pdb=" O GLU p 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 147 through 154 removed outlier: 6.811A pdb=" N ALA p 161 " --> pdb=" O ARG p 148 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL p 150 " --> pdb=" O VAL p 159 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL p 159 " --> pdb=" O VAL p 150 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR p 152 " --> pdb=" O ARG p 157 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ARG p 157 " --> pdb=" O TYR p 152 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY p 162 " --> pdb=" O THR p 166 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR p 166 " --> pdb=" O GLY p 162 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS p 171 " --> pdb=" O THR p 200 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR p 200 " --> pdb=" O LYS p 171 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 211 through 216 removed outlier: 6.553A pdb=" N ALA p 225 " --> pdb=" O VAL p 212 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE p 214 " --> pdb=" O LEU p 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU p 223 " --> pdb=" O ILE p 214 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL p 216 " --> pdb=" O ARG p 221 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG p 221 " --> pdb=" O VAL p 216 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER p 226 " --> pdb=" O SER p 230 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER p 230 " --> pdb=" O SER p 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'p' and resid 290 through 293 removed outlier: 3.519A pdb=" N SER p 307 " --> pdb=" O THR p 311 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR p 311 " --> pdb=" O SER p 307 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE p 312 " --> pdb=" O THR p 325 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR p 325 " --> pdb=" O ILE p 312 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR p 314 " --> pdb=" O ILE p 323 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'p' and resid 332 through 338 removed outlier: 4.161A pdb=" N HIS p 352 " --> pdb=" O SER p 348 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'p' and resid 378 through 383 removed outlier: 3.619A pdb=" N SER p 395 " --> pdb=" O THR p 399 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR p 399 " --> pdb=" O SER p 395 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR p 412 " --> pdb=" O VAL p 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'x' and resid 119 through 122 removed outlier: 6.162A pdb=" N GLN x 120 " --> pdb=" O ILE x 146 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER x 86 " --> pdb=" O LEU x 145 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY x 147 " --> pdb=" O SER x 86 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE x 88 " --> pdb=" O GLY x 147 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU x 87 " --> pdb=" O VAL x 170 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP x 172 " --> pdb=" O LEU x 87 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE x 89 " --> pdb=" O ASP x 172 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL x 47 " --> pdb=" O LEU x 201 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER x 203 " --> pdb=" O VAL x 47 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL x 49 " --> pdb=" O SER x 203 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP x 46 " --> pdb=" O VAL x 222 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE x 224 " --> pdb=" O ASP x 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL x 48 " --> pdb=" O ILE x 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'x' and resid 294 through 299 removed outlier: 6.365A pdb=" N LYS x 263 " --> pdb=" O LEU x 341 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE x 343 " --> pdb=" O LYS x 263 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE x 265 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N GLU x 394 " --> pdb=" O LEU x 236 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU x 238 " --> pdb=" O GLU x 394 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 538 hydrogen bonds 878 hydrogen bond angles 0 basepair planarities 213 basepair parallelities 345 stacking parallelities Total time for adding SS restraints: 13.50 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8763 1.33 - 1.45: 12294 1.45 - 1.57: 19026 1.57 - 1.70: 1383 1.70 - 1.82: 131 Bond restraints: 41597 Sorted by residual: bond pdb=" O5' C 11941 " pdb=" C5' C 11941 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.71e+00 bond pdb=" N9 G 11794 " pdb=" C4 G 11794 " ideal model delta sigma weight residual 1.375 1.401 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" O5' C 12050 " pdb=" C5' C 12050 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.71e+00 bond pdb=" O5' U 11942 " pdb=" C5' U 11942 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+00 bond pdb=" CA ARG P 135 " pdb=" C ARG P 135 " ideal model delta sigma weight residual 1.523 1.538 -0.016 1.23e-02 6.61e+03 1.65e+00 ... (remaining 41592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 58840 2.10 - 4.20: 520 4.20 - 6.30: 53 6.30 - 8.40: 9 8.40 - 10.50: 2 Bond angle restraints: 59424 Sorted by residual: angle pdb=" N ARG P 135 " pdb=" CA ARG P 135 " pdb=" C ARG P 135 " ideal model delta sigma weight residual 110.42 117.92 -7.50 1.46e+00 4.69e-01 2.64e+01 angle pdb=" N GLY P 134 " pdb=" CA GLY P 134 " pdb=" C GLY P 134 " ideal model delta sigma weight residual 112.73 117.72 -4.99 1.20e+00 6.94e-01 1.73e+01 angle pdb=" C ARG m 423 " pdb=" N PRO m 424 " pdb=" CA PRO m 424 " ideal model delta sigma weight residual 127.00 136.57 -9.57 2.40e+00 1.74e-01 1.59e+01 angle pdb=" C HIS P 133 " pdb=" CA HIS P 133 " pdb=" CB HIS P 133 " ideal model delta sigma weight residual 116.63 112.09 4.54 1.16e+00 7.43e-01 1.53e+01 angle pdb=" N LYS I 208 " pdb=" CA LYS I 208 " pdb=" C LYS I 208 " ideal model delta sigma weight residual 114.56 109.75 4.81 1.27e+00 6.20e-01 1.43e+01 ... (remaining 59419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 23197 35.72 - 71.44: 553 71.44 - 107.16: 46 107.16 - 142.88: 3 142.88 - 178.60: 3 Dihedral angle restraints: 23802 sinusoidal: 14911 harmonic: 8891 Sorted by residual: dihedral pdb=" O4' U 11764 " pdb=" C1' U 11764 " pdb=" N1 U 11764 " pdb=" C2 U 11764 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 11631 " pdb=" C1' C 11631 " pdb=" N1 C 11631 " pdb=" C2 C 11631 " ideal model delta sinusoidal sigma weight residual -160.00 -76.08 -83.92 1 1.50e+01 4.44e-03 3.81e+01 dihedral pdb=" CA GLY d 66 " pdb=" C GLY d 66 " pdb=" N VAL d 67 " pdb=" CA VAL d 67 " ideal model delta harmonic sigma weight residual 180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 23799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 6064 0.046 - 0.093: 912 0.093 - 0.139: 247 0.139 - 0.185: 30 0.185 - 0.231: 6 Chirality restraints: 7259 Sorted by residual: chirality pdb=" C1' G 11560 " pdb=" O4' G 11560 " pdb=" C2' G 11560 " pdb=" N9 G 11560 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' G 11525 " pdb=" O4' G 11525 " pdb=" C2' G 11525 " pdb=" N9 G 11525 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ARG P 135 " pdb=" N ARG P 135 " pdb=" C ARG P 135 " pdb=" CB ARG P 135 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 7256 not shown) Planarity restraints: 4902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 127 " 0.032 2.00e-02 2.50e+03 1.63e-02 5.95e+00 pdb=" N1 U 2 127 " -0.035 2.00e-02 2.50e+03 pdb=" C2 U 2 127 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U 2 127 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U 2 127 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U 2 127 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U 2 127 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U 2 127 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 127 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11602 " -0.030 2.00e-02 2.50e+03 1.38e-02 5.27e+00 pdb=" N9 A 11602 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A 11602 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 11602 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 11602 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A 11602 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 11602 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A 11602 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 11602 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11602 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 11602 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 11807 " -0.031 2.00e-02 2.50e+03 1.28e-02 4.88e+00 pdb=" N9 G 11807 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G 11807 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 11807 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 11807 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 11807 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 11807 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G 11807 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 11807 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 11807 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 11807 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 11807 " 0.006 2.00e-02 2.50e+03 ... (remaining 4899 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 306 2.59 - 3.16: 30331 3.16 - 3.74: 66555 3.74 - 4.32: 94794 4.32 - 4.90: 139966 Nonbonded interactions: 331952 Sorted by model distance: nonbonded pdb=" OP1 U 11924 " pdb=" NH2 ARG R 136 " model vdw 2.007 3.120 nonbonded pdb=" OG SER I 332 " pdb=" O LEU I 524 " model vdw 2.092 3.040 nonbonded pdb=" OG SER p 307 " pdb=" OD1 ASP p 309 " model vdw 2.110 3.040 nonbonded pdb=" OG SER p 395 " pdb=" OD1 ASP p 397 " model vdw 2.120 3.040 nonbonded pdb=" OP2 G 2 103 " pdb=" O2' A 2 105 " model vdw 2.124 3.040 ... (remaining 331947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 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: 6.460 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: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 45.660 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.003 0.039 41601 Z= 0.142 Angle : 0.532 10.496 59430 Z= 0.287 Chirality : 0.037 0.231 7259 Planarity : 0.004 0.047 4902 Dihedral : 13.975 178.602 17996 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 0.41 % Allowed : 1.29 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2946 helix: 1.68 (0.15), residues: 1214 sheet: 0.25 (0.23), residues: 532 loop : -0.35 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 168 TYR 0.018 0.001 TYR U 75 PHE 0.024 0.002 PHE x 61 TRP 0.023 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (41597) covalent geometry : angle 0.53123 / 0.29 (59424) hydrogen bonds : bond 0.12394 / 7.22 ( 1648) hydrogen bonds : angle 5.25106 / 2.91 ( 4064) metal coordination : bond 0.00397 / 0.25 ( 4) metal coordination : angle 2.82048 / 0.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 398 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 49 TYR cc_start: 0.8666 (p90) cc_final: 0.8428 (p90) REVERT: P 138 LYS cc_start: 0.7450 (ttpt) cc_final: 0.7001 (tptt) REVERT: U 104 ARG cc_start: 0.7773 (ptt180) cc_final: 0.7555 (ptt180) REVERT: k 36 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7946 (ttpt) REVERT: p 370 GLN cc_start: 0.7824 (pt0) cc_final: 0.7590 (mt0) REVERT: w 552 SER cc_start: 0.7862 (p) cc_final: 0.7631 (p) REVERT: x 241 CYS cc_start: 0.6151 (m) cc_final: 0.5835 (m) REVERT: x 345 LEU cc_start: 0.8017 (tp) cc_final: 0.7736 (mp) outliers start: 11 outliers final: 3 residues processed: 406 average time/residue: 0.2678 time to fit residues: 170.0366 Evaluate side-chains 302 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 292 ASN Chi-restraints excluded: chain x residue 435 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN X 137 ASN b 500 GLN j 30 GLN p 342 ASN ** p 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092116 restraints weight = 62333.944| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.21 r_work: 0.2936 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41601 Z= 0.140 Angle : 0.526 8.773 59430 Z= 0.274 Chirality : 0.037 0.222 7259 Planarity : 0.004 0.053 4902 Dihedral : 12.592 178.424 11656 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.11 % Allowed : 6.33 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2946 helix: 1.88 (0.15), residues: 1224 sheet: 0.27 (0.23), residues: 541 loop : -0.36 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG x 357 TYR 0.012 0.001 TYR x 276 PHE 0.024 0.002 PHE x 61 TRP 0.022 0.001 TRP m 464 HIS 0.005 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (41597) covalent geometry : angle 0.52468 / 0.27 (59424) hydrogen bonds : bond 0.04589 / 2.67 ( 1648) hydrogen bonds : angle 4.02382 / 2.26 ( 4064) metal coordination : bond 0.00460 / 0.29 ( 4) metal coordination : angle 3.01167 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 288 ASP cc_start: 0.7399 (t0) cc_final: 0.7198 (t0) REVERT: P 138 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7067 (tptt) REVERT: U 49 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7229 (t0) REVERT: k 36 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7880 (ttpt) REVERT: p 370 GLN cc_start: 0.8282 (pt0) cc_final: 0.7868 (mt0) REVERT: u 122 ARG cc_start: 0.7334 (mmp80) cc_final: 0.6882 (mmm-85) REVERT: w 552 SER cc_start: 0.7830 (p) cc_final: 0.7611 (p) REVERT: x 241 CYS cc_start: 0.6336 (m) cc_final: 0.6131 (m) REVERT: x 487 TRP cc_start: 0.7257 (m100) cc_final: 0.6914 (m100) outliers start: 30 outliers final: 22 residues processed: 333 average time/residue: 0.2593 time to fit residues: 134.6286 Evaluate side-chains 318 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 292 ASN Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 180 optimal weight: 0.0170 chunk 7 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 ASN Z 106 GLN c 71 GLN g 108 GLN p 255 ASN p 396 HIS t 25 ASN x 439 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088638 restraints weight = 62360.580| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.45 r_work: 0.2810 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 41601 Z= 0.307 Angle : 0.648 9.607 59430 Z= 0.338 Chirality : 0.044 0.305 7259 Planarity : 0.005 0.054 4902 Dihedral : 12.794 174.046 11654 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.81 % Allowed : 8.73 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2946 helix: 1.67 (0.15), residues: 1223 sheet: 0.01 (0.23), residues: 536 loop : -0.54 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 74 TYR 0.014 0.002 TYR n 572 PHE 0.028 0.003 PHE x 61 TRP 0.023 0.002 TRP m 464 HIS 0.007 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (41597) covalent geometry : angle 0.64714 / 0.34 (59424) hydrogen bonds : bond 0.05713 / 3.35 ( 1648) hydrogen bonds : angle 4.11260 / 2.30 ( 4064) metal coordination : bond 0.00982 / 0.59 ( 4) metal coordination : angle 3.02985 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 45 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7238 (ptpp) REVERT: 8 53 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7838 (tt0) REVERT: I 296 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: P 138 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7113 (tptt) REVERT: U 49 ASN cc_start: 0.7938 (t0) cc_final: 0.7559 (t0) REVERT: k 13 GLU cc_start: 0.8856 (tt0) cc_final: 0.8369 (tp30) REVERT: p 370 GLN cc_start: 0.8313 (pt0) cc_final: 0.7875 (mt0) REVERT: p 427 ASP cc_start: 0.7777 (t0) cc_final: 0.7444 (t0) REVERT: u 122 ARG cc_start: 0.7406 (mmp80) cc_final: 0.6914 (mmm-85) REVERT: w 451 LYS cc_start: 0.3402 (tttp) cc_final: 0.2413 (tttp) REVERT: x 466 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7248 (ttp-170) REVERT: x 487 TRP cc_start: 0.7332 (m100) cc_final: 0.7004 (m100) REVERT: x 498 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.4152 (t80) outliers start: 49 outliers final: 34 residues processed: 330 average time/residue: 0.2760 time to fit residues: 142.7567 Evaluate side-chains 327 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 349 THR Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 439 HIS Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 174 optimal weight: 0.6980 chunk 358 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN g 108 GLN j 30 GLN p 368 GLN t 25 ASN w 545 GLN ** x 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.085427 restraints weight = 62399.950| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.28 r_work: 0.2810 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 41601 Z= 0.280 Angle : 0.616 9.223 59430 Z= 0.321 Chirality : 0.042 0.307 7259 Planarity : 0.005 0.054 4902 Dihedral : 12.833 172.856 11652 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.11 % Allowed : 10.95 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 2946 helix: 1.59 (0.15), residues: 1225 sheet: -0.06 (0.22), residues: 536 loop : -0.68 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 74 TYR 0.012 0.002 TYR x 276 PHE 0.026 0.002 PHE x 61 TRP 0.018 0.002 TRP m 464 HIS 0.033 0.002 HIS x 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (41597) covalent geometry : angle 0.61556 / 0.32 (59424) hydrogen bonds : bond 0.05397 / 3.17 ( 1648) hydrogen bonds : angle 4.06591 / 2.28 ( 4064) metal coordination : bond 0.00849 / 0.53 ( 4) metal coordination : angle 2.93591 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7750 (tt0) REVERT: I 296 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: P 138 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7167 (tptt) REVERT: d 11 GLU cc_start: 0.5382 (pm20) cc_final: 0.5145 (pm20) REVERT: k 13 GLU cc_start: 0.8754 (tt0) cc_final: 0.8247 (tp30) REVERT: p 370 GLN cc_start: 0.8217 (pt0) cc_final: 0.7780 (mt0) REVERT: u 122 ARG cc_start: 0.7365 (mmp80) cc_final: 0.6933 (mmm-85) REVERT: w 387 MET cc_start: 0.4069 (mmp) cc_final: 0.3361 (mtt) REVERT: w 451 LYS cc_start: 0.3108 (tttp) cc_final: 0.1918 (tttp) REVERT: x 108 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7747 (mt-10) REVERT: x 498 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.4228 (t80) REVERT: x 523 LYS cc_start: 0.6893 (mtmm) cc_final: 0.6111 (tptp) outliers start: 57 outliers final: 40 residues processed: 327 average time/residue: 0.2692 time to fit residues: 136.9048 Evaluate side-chains 326 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 496 ILE Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 683 LEU Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 697 ASP Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 116 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 279 optimal weight: 0.0870 chunk 214 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 GLN g 108 GLN j 30 GLN t 25 ASN x 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090449 restraints weight = 62232.449| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.28 r_work: 0.2845 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41601 Z= 0.137 Angle : 0.508 8.175 59430 Z= 0.266 Chirality : 0.037 0.211 7259 Planarity : 0.004 0.055 4902 Dihedral : 12.706 176.278 11652 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.78 % Allowed : 11.99 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2946 helix: 1.93 (0.15), residues: 1215 sheet: 0.04 (0.22), residues: 545 loop : -0.61 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 74 TYR 0.010 0.001 TYR p 152 PHE 0.023 0.001 PHE x 61 TRP 0.031 0.002 TRP x 487 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (41597) covalent geometry : angle 0.50730 / 0.27 (59424) hydrogen bonds : bond 0.04402 / 2.58 ( 1648) hydrogen bonds : angle 3.81296 / 2.14 ( 4064) metal coordination : bond 0.00397 / 0.26 ( 4) metal coordination : angle 2.97530 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 288 ASP cc_start: 0.7416 (t0) cc_final: 0.7159 (t0) REVERT: I 296 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: I 439 MET cc_start: 0.9001 (mmp) cc_final: 0.8525 (mmp) REVERT: P 138 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7248 (tptt) REVERT: R 144 GLN cc_start: 0.8126 (tp40) cc_final: 0.7904 (tp-100) REVERT: R 148 ASP cc_start: 0.7876 (m-30) cc_final: 0.7671 (m-30) REVERT: Z 109 GLU cc_start: 0.8605 (tp30) cc_final: 0.7902 (pt0) REVERT: p 370 GLN cc_start: 0.8311 (pt0) cc_final: 0.7870 (mt0) REVERT: u 104 GLU cc_start: 0.4027 (OUTLIER) cc_final: 0.3515 (mp0) REVERT: u 122 ARG cc_start: 0.7405 (mmp80) cc_final: 0.7045 (mmm-85) REVERT: w 451 LYS cc_start: 0.2717 (tttp) cc_final: 0.2062 (tttp) REVERT: x 108 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7786 (mt-10) REVERT: x 487 TRP cc_start: 0.7106 (m100) cc_final: 0.6820 (m100) REVERT: x 498 TYR cc_start: 0.5325 (OUTLIER) cc_final: 0.4182 (t80) REVERT: x 523 LYS cc_start: 0.6851 (mtmm) cc_final: 0.6028 (tptp) outliers start: 48 outliers final: 34 residues processed: 338 average time/residue: 0.2866 time to fit residues: 151.9107 Evaluate side-chains 327 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 221 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 295 optimal weight: 0.6980 chunk 303 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 299 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN Z 123 GLN c 71 GLN g 108 GLN j 30 GLN t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089600 restraints weight = 62336.622| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.27 r_work: 0.2874 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41601 Z= 0.126 Angle : 0.490 8.331 59430 Z= 0.257 Chirality : 0.036 0.203 7259 Planarity : 0.004 0.054 4902 Dihedral : 12.599 177.927 11652 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.11 % Allowed : 12.62 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2946 helix: 2.04 (0.15), residues: 1216 sheet: 0.09 (0.22), residues: 544 loop : -0.57 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 466 TYR 0.010 0.001 TYR p 152 PHE 0.023 0.001 PHE x 61 TRP 0.017 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (41597) covalent geometry : angle 0.48955 / 0.26 (59424) hydrogen bonds : bond 0.04254 / 2.49 ( 1648) hydrogen bonds : angle 3.71634 / 2.08 ( 4064) metal coordination : bond 0.00365 / 0.23 ( 4) metal coordination : angle 2.94389 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7880 (tt0) REVERT: I 288 ASP cc_start: 0.7393 (t0) cc_final: 0.7053 (t0) REVERT: I 296 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: I 439 MET cc_start: 0.9040 (mmp) cc_final: 0.8679 (mmp) REVERT: P 138 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7292 (tptt) REVERT: R 152 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6332 (tt0) REVERT: X 73 MET cc_start: 0.8719 (mmm) cc_final: 0.8455 (mmm) REVERT: Z 109 GLU cc_start: 0.8564 (tp30) cc_final: 0.7851 (pt0) REVERT: k 76 ASN cc_start: 0.8662 (m-40) cc_final: 0.8460 (t0) REVERT: p 370 GLN cc_start: 0.8291 (pt0) cc_final: 0.7992 (mt0) REVERT: u 122 ARG cc_start: 0.7384 (mmp80) cc_final: 0.7097 (mmm-85) REVERT: w 451 LYS cc_start: 0.2058 (tttp) cc_final: 0.1467 (tttp) REVERT: x 108 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7729 (mt-10) REVERT: x 498 TYR cc_start: 0.5270 (OUTLIER) cc_final: 0.4151 (t80) REVERT: x 523 LYS cc_start: 0.6908 (mtmm) cc_final: 0.6153 (tptp) outliers start: 57 outliers final: 36 residues processed: 340 average time/residue: 0.2812 time to fit residues: 150.8776 Evaluate side-chains 335 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 256 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 198 optimal weight: 0.0370 chunk 62 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN Z 123 GLN c 71 GLN g 108 GLN p 426 ASN t 25 ASN u 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089775 restraints weight = 62303.141| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.43 r_work: 0.2829 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41601 Z= 0.147 Angle : 0.503 12.442 59430 Z= 0.263 Chirality : 0.037 0.269 7259 Planarity : 0.004 0.054 4902 Dihedral : 12.574 177.959 11652 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.11 % Allowed : 12.69 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.16), residues: 2946 helix: 2.05 (0.15), residues: 1216 sheet: 0.08 (0.22), residues: 549 loop : -0.56 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 8 52 TYR 0.009 0.001 TYR R 124 PHE 0.023 0.001 PHE x 61 TRP 0.016 0.001 TRP m 464 HIS 0.005 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (41597) covalent geometry : angle 0.50195 / 0.26 (59424) hydrogen bonds : bond 0.04373 / 2.56 ( 1648) hydrogen bonds : angle 3.72846 / 2.10 ( 4064) metal coordination : bond 0.00469 / 0.29 ( 4) metal coordination : angle 2.96621 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 303 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7953 (tt0) REVERT: I 288 ASP cc_start: 0.7480 (t0) cc_final: 0.7120 (t0) REVERT: I 296 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: I 439 MET cc_start: 0.9026 (mmp) cc_final: 0.8645 (mmp) REVERT: P 138 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7311 (tptt) REVERT: R 152 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: X 73 MET cc_start: 0.8803 (mmm) cc_final: 0.8550 (mmm) REVERT: Z 109 GLU cc_start: 0.8645 (tp30) cc_final: 0.7898 (pt0) REVERT: c 76 GLU cc_start: 0.8190 (mp0) cc_final: 0.7916 (mp0) REVERT: k 76 ASN cc_start: 0.8737 (m-40) cc_final: 0.8521 (t0) REVERT: p 237 ILE cc_start: 0.7627 (mp) cc_final: 0.7386 (mm) REVERT: p 370 GLN cc_start: 0.8366 (pt0) cc_final: 0.8073 (mt0) REVERT: w 387 MET cc_start: 0.3616 (mmp) cc_final: 0.2948 (mtt) REVERT: w 451 LYS cc_start: 0.2483 (tttp) cc_final: 0.1687 (tttp) REVERT: x 108 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7797 (mt-10) REVERT: x 498 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.4192 (t80) REVERT: x 523 LYS cc_start: 0.6972 (mtmm) cc_final: 0.6266 (tptp) outliers start: 57 outliers final: 44 residues processed: 336 average time/residue: 0.2786 time to fit residues: 148.3675 Evaluate side-chains 342 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 69 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 199 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 157 optimal weight: 0.0870 chunk 184 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN Z 123 GLN c 71 GLN g 108 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086642 restraints weight = 62088.133| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.22 r_work: 0.2836 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41601 Z= 0.204 Angle : 0.547 10.357 59430 Z= 0.286 Chirality : 0.039 0.313 7259 Planarity : 0.004 0.056 4902 Dihedral : 12.630 176.381 11652 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.37 % Allowed : 12.80 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2946 helix: 1.95 (0.15), residues: 1216 sheet: 0.01 (0.22), residues: 541 loop : -0.61 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 8 52 TYR 0.010 0.001 TYR X 103 PHE 0.024 0.002 PHE x 61 TRP 0.016 0.002 TRP m 464 HIS 0.006 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (41597) covalent geometry : angle 0.54610 / 0.29 (59424) hydrogen bonds : bond 0.04814 / 2.83 ( 1648) hydrogen bonds : angle 3.82402 / 2.14 ( 4064) metal coordination : bond 0.00695 / 0.43 ( 4) metal coordination : angle 2.95821 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 294 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7850 (tt0) REVERT: I 288 ASP cc_start: 0.7501 (t0) cc_final: 0.7138 (t0) REVERT: I 296 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: I 439 MET cc_start: 0.8981 (mmp) cc_final: 0.8562 (mmp) REVERT: P 138 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7256 (tptt) REVERT: R 152 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: X 21 LYS cc_start: 0.6826 (mtpt) cc_final: 0.5071 (pttp) REVERT: c 47 ASN cc_start: 0.7690 (t0) cc_final: 0.7473 (t0) REVERT: g 70 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9165 (pttp) REVERT: p 370 GLN cc_start: 0.8285 (pt0) cc_final: 0.7991 (mt0) REVERT: w 451 LYS cc_start: 0.2100 (tttp) cc_final: 0.1560 (tttp) REVERT: x 108 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7718 (mt-10) REVERT: x 498 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.4195 (t80) REVERT: x 523 LYS cc_start: 0.6934 (mtmm) cc_final: 0.6124 (tptp) outliers start: 64 outliers final: 43 residues processed: 333 average time/residue: 0.2797 time to fit residues: 147.1359 Evaluate side-chains 336 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 697 ASP Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 69 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.9980 chunk 90 optimal weight: 0.0020 chunk 31 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 GLN c 71 GLN j 30 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090484 restraints weight = 62536.413| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.25 r_work: 0.2902 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 41601 Z= 0.105 Angle : 0.485 10.110 59430 Z= 0.254 Chirality : 0.035 0.307 7259 Planarity : 0.003 0.055 4902 Dihedral : 12.586 178.741 11652 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.66 % Allowed : 13.43 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2946 helix: 2.13 (0.15), residues: 1214 sheet: 0.05 (0.22), residues: 550 loop : -0.55 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 52 TYR 0.010 0.001 TYR p 304 PHE 0.023 0.001 PHE x 61 TRP 0.017 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (41597) covalent geometry : angle 0.48392 / 0.25 (59424) hydrogen bonds : bond 0.04080 / 2.39 ( 1648) hydrogen bonds : angle 3.68023 / 2.06 ( 4064) metal coordination : bond 0.00276 / 0.18 ( 4) metal coordination : angle 2.92103 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7820 (tt0) REVERT: I 280 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8313 (tt) REVERT: I 288 ASP cc_start: 0.7438 (t0) cc_final: 0.7068 (t0) REVERT: I 296 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: I 439 MET cc_start: 0.8950 (mmp) cc_final: 0.8467 (mmp) REVERT: P 138 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7253 (tptt) REVERT: R 152 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: X 73 MET cc_start: 0.8679 (mmm) cc_final: 0.8444 (mmm) REVERT: c 76 GLU cc_start: 0.8034 (mp0) cc_final: 0.7746 (mp0) REVERT: k 76 ASN cc_start: 0.8632 (m-40) cc_final: 0.8430 (t0) REVERT: p 370 GLN cc_start: 0.8330 (pt0) cc_final: 0.8026 (mt0) REVERT: u 122 ARG cc_start: 0.7512 (mmp80) cc_final: 0.6879 (mmm-85) REVERT: w 451 LYS cc_start: 0.2161 (tttp) cc_final: 0.1503 (tttp) REVERT: x 363 ARG cc_start: 0.5004 (mmt-90) cc_final: 0.4585 (mmt90) REVERT: x 498 TYR cc_start: 0.5230 (OUTLIER) cc_final: 0.4085 (t80) REVERT: x 523 LYS cc_start: 0.6932 (mtmm) cc_final: 0.6127 (tptp) outliers start: 45 outliers final: 32 residues processed: 331 average time/residue: 0.2710 time to fit residues: 141.9556 Evaluate side-chains 331 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 154 optimal weight: 0.9980 chunk 269 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 339 optimal weight: 0.5980 chunk 325 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 221 optimal weight: 0.0030 chunk 67 optimal weight: 5.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 56 GLN Z 123 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093115 restraints weight = 62170.099| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.28 r_work: 0.2934 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41601 Z= 0.092 Angle : 0.470 9.772 59430 Z= 0.246 Chirality : 0.034 0.310 7259 Planarity : 0.003 0.055 4902 Dihedral : 12.548 179.554 11652 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.44 % Allowed : 13.76 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2946 helix: 2.20 (0.15), residues: 1217 sheet: 0.13 (0.23), residues: 551 loop : -0.51 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG u 137 TYR 0.012 0.001 TYR p 304 PHE 0.022 0.001 PHE x 61 TRP 0.017 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (41597) covalent geometry : angle 0.46929 / 0.25 (59424) hydrogen bonds : bond 0.03869 / 2.27 ( 1648) hydrogen bonds : angle 3.60958 / 2.02 ( 4064) metal coordination : bond 0.00224 / 0.14 ( 4) metal coordination : angle 3.09497 / 1.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 280 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8269 (tt) REVERT: I 288 ASP cc_start: 0.7397 (t0) cc_final: 0.7045 (t0) REVERT: I 296 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: I 439 MET cc_start: 0.8910 (mmp) cc_final: 0.8443 (mmp) REVERT: P 138 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7240 (tptt) REVERT: R 152 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: U 44 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7317 (tt0) REVERT: c 76 GLU cc_start: 0.8101 (mp0) cc_final: 0.7774 (mp0) REVERT: m 487 HIS cc_start: 0.8440 (m90) cc_final: 0.8226 (m90) REVERT: p 370 GLN cc_start: 0.8301 (pt0) cc_final: 0.8024 (mt0) REVERT: u 57 LYS cc_start: 0.8576 (mttp) cc_final: 0.8066 (mmtt) REVERT: u 122 ARG cc_start: 0.7453 (mmp80) cc_final: 0.6791 (mmm-85) REVERT: w 451 LYS cc_start: 0.2120 (tttp) cc_final: 0.1383 (tttt) REVERT: x 363 ARG cc_start: 0.5045 (mmt-90) cc_final: 0.4626 (mmt90) REVERT: x 498 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4120 (t80) outliers start: 39 outliers final: 29 residues processed: 326 average time/residue: 0.2698 time to fit residues: 139.8811 Evaluate side-chains 326 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 349 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN Z 123 GLN c 71 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088177 restraints weight = 62199.159| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.31 r_work: 0.2849 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41601 Z= 0.191 Angle : 0.527 9.479 59430 Z= 0.275 Chirality : 0.038 0.298 7259 Planarity : 0.004 0.054 4902 Dihedral : 12.552 178.116 11652 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.70 % Allowed : 13.61 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2946 helix: 2.06 (0.15), residues: 1219 sheet: 0.01 (0.22), residues: 553 loop : -0.55 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 8 52 TYR 0.014 0.001 TYR I 346 PHE 0.025 0.002 PHE x 61 TRP 0.016 0.002 TRP m 464 HIS 0.006 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (41597) covalent geometry : angle 0.52632 / 0.28 (59424) hydrogen bonds : bond 0.04591 / 2.69 ( 1648) hydrogen bonds : angle 3.74348 / 2.09 ( 4064) metal coordination : bond 0.00640 / 0.39 ( 4) metal coordination : angle 2.99850 / 1.00 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12886.86 seconds wall clock time: 220 minutes 36.52 seconds (13236.52 seconds total)