Starting phenix.real_space_refine on Sat Aug 23 11:28:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uib_42291/08_2025/8uib_42291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uib_42291/08_2025/8uib_42291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uib_42291/08_2025/8uib_42291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uib_42291/08_2025/8uib_42291.map" model { file = "/net/cci-nas-00/data/ceres_data/8uib_42291/08_2025/8uib_42291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uib_42291/08_2025/8uib_42291.cif" } resolution = 3.21 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= 0.008 sd= 0.093 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 92 5.16 5 C 7590 2.51 5 N 2004 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11868 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3173 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 32, 'TRANS': 374} Chain breaks: 9 Chain: "K" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3375 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5318 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 660} Chain breaks: 7 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11853 SG CYS T 820 27.443 51.633 48.456 1.00 33.04 S Time building chain proxies: 2.86, per 1000 atoms: 0.24 Number of scatterers: 11868 At special positions: 0 Unit cell: (88.81, 102.92, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 92 16.00 O 2180 8.00 N 2004 7.00 C 7590 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: 1.00 Conformation dependent library (CDL) restraints added in 594.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" ND1 HIS K 70 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 157 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 68 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" SG CYS T 820 " pdb="ZN ZN K 802 " - pdb=" NE2 HIS K 414 " pdb="ZN ZN K 802 " - pdb=" NE2 HIS K 73 " 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 53.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'I' and resid 32 through 38 removed outlier: 3.666A pdb=" N LEU I 36 " --> pdb=" O THR I 33 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE I 38 " --> pdb=" O THR I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 115 removed outlier: 3.739A pdb=" N ILE I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 115 " --> pdb=" O PRO I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 146 removed outlier: 3.933A pdb=" N ILE I 132 " --> pdb=" O PRO I 128 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 136 " --> pdb=" O ILE I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 192 Processing helix chain 'I' and resid 273 through 290 removed outlier: 3.906A pdb=" N ASN I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR I 288 " --> pdb=" O ASN I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 320 removed outlier: 4.258A pdb=" N ASP I 307 " --> pdb=" O GLY I 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS I 311 " --> pdb=" O ASP I 307 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN I 314 " --> pdb=" O GLU I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 340 Processing helix chain 'I' and resid 382 through 386 Processing helix chain 'I' and resid 404 through 413 Processing helix chain 'I' and resid 433 through 437 Processing helix chain 'I' and resid 453 through 465 Processing helix chain 'I' and resid 474 through 476 No H-bonds generated for 'chain 'I' and resid 474 through 476' Processing helix chain 'K' and resid 57 through 60 No H-bonds generated for 'chain 'K' and resid 57 through 60' Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 95 through 114 Proline residue: K 101 - end of helix removed outlier: 3.772A pdb=" N GLU K 105 " --> pdb=" O PRO K 101 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 131 Processing helix chain 'K' and resid 216 through 228 removed outlier: 3.752A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 259 removed outlier: 3.889A pdb=" N ILE K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU K 251 " --> pdb=" O GLU K 247 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 288 removed outlier: 3.758A pdb=" N LEU K 281 " --> pdb=" O HIS K 277 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE K 283 " --> pdb=" O TYR K 279 " (cutoff:3.500A) Proline residue: K 284 - end of helix Processing helix chain 'K' and resid 325 through 329 removed outlier: 4.098A pdb=" N LEU K 328 " --> pdb=" O PRO K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 341 removed outlier: 3.531A pdb=" N ALA K 341 " --> pdb=" O PHE K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 366 removed outlier: 3.538A pdb=" N LYS K 362 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY K 366 " --> pdb=" O LYS K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 406 removed outlier: 3.542A pdb=" N MET K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 430 removed outlier: 3.907A pdb=" N PHE K 422 " --> pdb=" O LYS K 418 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 17 removed outlier: 4.097A pdb=" N VAL T 17 " --> pdb=" O CYS T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 40 removed outlier: 3.695A pdb=" N GLU T 30 " --> pdb=" O ASP T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 52 Processing helix chain 'T' and resid 53 through 65 removed outlier: 3.572A pdb=" N GLU T 57 " --> pdb=" O PRO T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 84 Processing helix chain 'T' and resid 86 through 93 Processing helix chain 'T' and resid 98 through 104 Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.522A pdb=" N ARG T 111 " --> pdb=" O PRO T 108 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA T 112 " --> pdb=" O LEU T 109 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR T 113 " --> pdb=" O GLY T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 131 removed outlier: 3.639A pdb=" N GLN T 125 " --> pdb=" O SER T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 133 through 143 removed outlier: 3.573A pdb=" N HIS T 143 " --> pdb=" O PHE T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 146 through 153 Processing helix chain 'T' and resid 157 through 176 removed outlier: 3.519A pdb=" N SER T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA T 163 " --> pdb=" O PHE T 159 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN T 166 " --> pdb=" O SER T 162 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 207 removed outlier: 3.769A pdb=" N MET T 199 " --> pdb=" O ALA T 195 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 228 removed outlier: 3.653A pdb=" N THR T 223 " --> pdb=" O ASN T 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS T 228 " --> pdb=" O THR T 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 246 Proline residue: T 242 - end of helix Processing helix chain 'T' and resid 247 through 250 Processing helix chain 'T' and resid 255 through 267 Processing helix chain 'T' and resid 276 through 278 No H-bonds generated for 'chain 'T' and resid 276 through 278' Processing helix chain 'T' and resid 279 through 290 removed outlier: 3.816A pdb=" N SER T 288 " --> pdb=" O ALA T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 294 through 304 removed outlier: 3.557A pdb=" N LEU T 298 " --> pdb=" O HIS T 294 " (cutoff:3.500A) Processing helix chain 'T' and resid 309 through 322 removed outlier: 3.772A pdb=" N GLN T 315 " --> pdb=" O ALA T 311 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU T 320 " --> pdb=" O ALA T 316 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN T 322 " --> pdb=" O GLN T 318 " (cutoff:3.500A) Processing helix chain 'T' and resid 323 through 325 No H-bonds generated for 'chain 'T' and resid 323 through 325' Processing helix chain 'T' and resid 348 through 355 removed outlier: 4.740A pdb=" N THR T 353 " --> pdb=" O THR T 349 " (cutoff:3.500A) Processing helix chain 'T' and resid 357 through 376 Processing helix chain 'T' and resid 386 through 402 Processing helix chain 'T' and resid 409 through 419 removed outlier: 3.859A pdb=" N GLY T 417 " --> pdb=" O GLY T 413 " (cutoff:3.500A) Processing helix chain 'T' and resid 422 through 436 Processing helix chain 'T' and resid 442 through 458 removed outlier: 3.731A pdb=" N VAL T 446 " --> pdb=" O PRO T 442 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL T 452 " --> pdb=" O GLN T 448 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) Processing helix chain 'T' and resid 463 through 479 Processing helix chain 'T' and resid 494 through 510 removed outlier: 3.676A pdb=" N GLU T 500 " --> pdb=" O GLN T 496 " (cutoff:3.500A) Proline residue: T 503 - end of helix removed outlier: 3.975A pdb=" N LYS T 507 " --> pdb=" O PRO T 503 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 528 Processing helix chain 'T' and resid 534 through 539 Processing helix chain 'T' and resid 546 through 551 Processing helix chain 'T' and resid 552 through 556 removed outlier: 3.787A pdb=" N GLN T 555 " --> pdb=" O GLN T 552 " (cutoff:3.500A) Processing helix chain 'T' and resid 558 through 567 Processing helix chain 'T' and resid 567 through 575 removed outlier: 3.532A pdb=" N SER T 573 " --> pdb=" O MET T 569 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN T 575 " --> pdb=" O GLN T 571 " (cutoff:3.500A) Processing helix chain 'T' and resid 591 through 603 removed outlier: 3.617A pdb=" N ASP T 603 " --> pdb=" O ILE T 599 " (cutoff:3.500A) Processing helix chain 'T' and resid 606 through 623 Processing helix chain 'T' and resid 624 through 628 Processing helix chain 'T' and resid 630 through 644 removed outlier: 3.616A pdb=" N VAL T 635 " --> pdb=" O THR T 631 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN T 640 " --> pdb=" O ALA T 636 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA T 641 " --> pdb=" O THR T 637 " (cutoff:3.500A) Processing helix chain 'T' and resid 647 through 666 removed outlier: 3.795A pdb=" N ARG T 651 " --> pdb=" O ASP T 647 " (cutoff:3.500A) Processing helix chain 'T' and resid 693 through 697 removed outlier: 3.653A pdb=" N HIS T 697 " --> pdb=" O ALA T 694 " (cutoff:3.500A) Processing helix chain 'T' and resid 702 through 709 removed outlier: 4.174A pdb=" N PHE T 709 " --> pdb=" O PHE T 705 " (cutoff:3.500A) Processing helix chain 'T' and resid 712 through 725 Processing helix chain 'T' and resid 774 through 779 removed outlier: 3.873A pdb=" N SER T 778 " --> pdb=" O ALA T 774 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU T 779 " --> pdb=" O MET T 775 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 774 through 779' Processing helix chain 'T' and resid 780 through 788 Processing helix chain 'T' and resid 798 through 808 Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.697A pdb=" N GLU I 503 " --> pdb=" O LEU I 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 24 through 25 removed outlier: 7.532A pdb=" N MET I 25 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE I 99 " --> pdb=" O TYR I 124 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL I 123 " --> pdb=" O GLN I 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'I' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'I' and resid 210 through 215 removed outlier: 3.860A pdb=" N GLN I 210 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 260 through 262 removed outlier: 5.897A pdb=" N LEU I 261 " --> pdb=" O VAL I 470 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET I 497 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N CYS I 471 " --> pdb=" O MET I 497 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'I' and resid 295 through 296 removed outlier: 6.257A pdb=" N VAL I 295 " --> pdb=" O VAL I 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 326 through 329 removed outlier: 6.701A pdb=" N LEU I 326 " --> pdb=" O LYS I 374 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR I 376 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE I 328 " --> pdb=" O TYR I 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 419 through 422 Processing sheet with id=AA9, first strand: chain 'K' and resid 90 through 91 removed outlier: 8.186A pdb=" N TYR K 91 " --> pdb=" O ASP K 62 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL K 64 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN K 28 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE K 65 " --> pdb=" O ASN K 28 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET K 30 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE K 4 " --> pdb=" O LEU K 446 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 141 through 143 removed outlier: 7.093A pdb=" N SER K 172 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE K 201 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL K 174 " --> pdb=" O ILE K 201 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU K 200 " --> pdb=" O LEU K 411 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL K 410 " --> pdb=" O TYR K 436 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 319 through 323 removed outlier: 6.014A pdb=" N LYS K 234 " --> pdb=" O MET K 347 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 349 " --> pdb=" O LYS K 234 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU K 236 " --> pdb=" O ILE K 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 369 through 370 removed outlier: 3.643A pdb=" N LEU K 370 " --> pdb=" O LEU K 378 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1949 1.31 - 1.44: 3102 1.44 - 1.57: 6938 1.57 - 1.69: 0 1.69 - 1.82: 132 Bond restraints: 12121 Sorted by residual: bond pdb=" C CYS K 100 " pdb=" O CYS K 100 " ideal model delta sigma weight residual 1.244 1.190 0.054 9.80e-03 1.04e+04 2.98e+01 bond pdb=" C PRO K 101 " pdb=" O PRO K 101 " ideal model delta sigma weight residual 1.236 1.184 0.053 1.36e-02 5.41e+03 1.51e+01 bond pdb=" C TYR K 107 " pdb=" O TYR K 107 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.40e+01 bond pdb=" C ALA K 111 " pdb=" O ALA K 111 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.26e-02 6.30e+03 1.24e+01 bond pdb=" N ILE K 102 " pdb=" CA ILE K 102 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.22e-02 6.72e+03 1.19e+01 ... (remaining 12116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15868 2.19 - 4.37: 473 4.37 - 6.56: 90 6.56 - 8.74: 20 8.74 - 10.93: 5 Bond angle restraints: 16456 Sorted by residual: angle pdb=" CA ASP K 106 " pdb=" CB ASP K 106 " pdb=" CG ASP K 106 " ideal model delta sigma weight residual 112.60 120.30 -7.70 1.00e+00 1.00e+00 5.93e+01 angle pdb=" N LYS K 114 " pdb=" CA LYS K 114 " pdb=" C LYS K 114 " ideal model delta sigma weight residual 113.02 104.56 8.46 1.20e+00 6.94e-01 4.97e+01 angle pdb=" CA ASP K 113 " pdb=" CB ASP K 113 " pdb=" CG ASP K 113 " ideal model delta sigma weight residual 112.60 119.56 -6.96 1.00e+00 1.00e+00 4.84e+01 angle pdb=" N GLU K 105 " pdb=" CA GLU K 105 " pdb=" C GLU K 105 " ideal model delta sigma weight residual 113.16 106.35 6.81 1.24e+00 6.50e-01 3.02e+01 angle pdb=" N VAL T 146 " pdb=" CA VAL T 146 " pdb=" C VAL T 146 " ideal model delta sigma weight residual 112.96 107.51 5.45 1.00e+00 1.00e+00 2.97e+01 ... (remaining 16451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 6410 16.81 - 33.63: 677 33.63 - 50.44: 151 50.44 - 67.26: 35 67.26 - 84.07: 10 Dihedral angle restraints: 7283 sinusoidal: 2856 harmonic: 4427 Sorted by residual: dihedral pdb=" CA ASN I 284 " pdb=" C ASN I 284 " pdb=" N LEU I 285 " pdb=" CA LEU I 285 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ILE K 24 " pdb=" C ILE K 24 " pdb=" N ALA K 25 " pdb=" CA ALA K 25 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" N MET K 92 " pdb=" C MET K 92 " pdb=" CA MET K 92 " pdb=" CB MET K 92 " ideal model delta harmonic sigma weight residual 122.80 111.22 11.58 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 7280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1673 0.080 - 0.160: 214 0.160 - 0.241: 17 0.241 - 0.321: 3 0.321 - 0.401: 2 Chirality restraints: 1909 Sorted by residual: chirality pdb=" CA MET K 92 " pdb=" N MET K 92 " pdb=" C MET K 92 " pdb=" CB MET K 92 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ASP K 106 " pdb=" N ASP K 106 " pdb=" C ASP K 106 " pdb=" CB ASP K 106 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA TYR K 107 " pdb=" N TYR K 107 " pdb=" C TYR K 107 " pdb=" CB TYR K 107 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1906 not shown) Planarity restraints: 2093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE T 616 " -0.029 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE T 616 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE T 616 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE T 616 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE T 616 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE T 616 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE T 616 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO K 95 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO K 95 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO K 95 " 0.021 2.00e-02 2.50e+03 pdb=" N THR K 96 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER T 230 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO T 231 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO T 231 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO T 231 " 0.038 5.00e-02 4.00e+02 ... (remaining 2090 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 129 2.59 - 3.17: 9735 3.17 - 3.75: 18705 3.75 - 4.32: 26298 4.32 - 4.90: 44196 Nonbonded interactions: 99063 Sorted by model distance: nonbonded pdb=" OD2 ASP K 72 " pdb="ZN ZN K 802 " model vdw 2.018 2.230 nonbonded pdb=" OD2 ASP K 178 " pdb="ZN ZN K 801 " model vdw 2.058 2.230 nonbonded pdb=" O SER T 278 " pdb=" OG1 THR T 282 " model vdw 2.199 3.040 nonbonded pdb=" O LEU I 400 " pdb=" OH TYR I 436 " model vdw 2.203 3.040 nonbonded pdb=" O SER T 230 " pdb=" OG1 THR T 233 " model vdw 2.212 3.040 ... (remaining 99058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12127 Z= 0.295 Angle : 0.921 10.927 16456 Z= 0.510 Chirality : 0.055 0.401 1909 Planarity : 0.007 0.069 2093 Dihedral : 15.061 84.070 4405 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.84 % Allowed : 0.46 % Favored : 98.71 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -2.75 (0.20), residues: 1489 helix: -1.45 (0.17), residues: 769 sheet: -1.95 (0.42), residues: 140 loop : -2.14 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 367 TYR 0.029 0.003 TYR K 107 PHE 0.064 0.003 PHE T 616 TRP 0.018 0.002 TRP I 225 HIS 0.008 0.001 HIS K 137 Details of bonding type rmsd covalent geometry : bond 0.00627 (12121) covalent geometry : angle 0.92103 (16456) hydrogen bonds : bond 0.15096 ( 509) hydrogen bonds : angle 6.98387 ( 1449) metal coordination : bond 0.00616 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 167 average time/residue: 0.1128 time to fit residues: 27.2998 Evaluate side-chains 123 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 226 HIS ** K 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146080 restraints weight = 16320.752| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.60 r_work: 0.3762 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12127 Z= 0.202 Angle : 0.688 10.827 16456 Z= 0.345 Chirality : 0.045 0.182 1909 Planarity : 0.006 0.061 2093 Dihedral : 5.926 53.369 1619 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.84 % Allowed : 9.89 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -2.22 (0.21), residues: 1489 helix: -0.88 (0.18), residues: 796 sheet: -1.80 (0.44), residues: 136 loop : -2.11 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 562 TYR 0.050 0.002 TYR K 107 PHE 0.033 0.002 PHE T 616 TRP 0.011 0.002 TRP T 237 HIS 0.005 0.001 HIS K 157 Details of bonding type rmsd covalent geometry : bond 0.00488 (12121) covalent geometry : angle 0.68788 (16456) hydrogen bonds : bond 0.03859 ( 509) hydrogen bonds : angle 5.16504 ( 1449) metal coordination : bond 0.00571 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 107 TYR cc_start: 0.7135 (t80) cc_final: 0.6870 (t80) REVERT: K 130 MET cc_start: 0.8388 (mmm) cc_final: 0.8110 (mmp) REVERT: T 91 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: T 616 PHE cc_start: 0.6188 (m-80) cc_final: 0.5985 (m-80) REVERT: T 775 MET cc_start: 0.7542 (tpt) cc_final: 0.7239 (tpt) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.0986 time to fit residues: 21.2801 Evaluate side-chains 125 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 224 ASN ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.168279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148614 restraints weight = 16217.308| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.65 r_work: 0.3808 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12127 Z= 0.132 Angle : 0.605 11.162 16456 Z= 0.301 Chirality : 0.043 0.173 1909 Planarity : 0.005 0.059 2093 Dihedral : 5.480 49.782 1619 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.44 % Allowed : 12.40 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.62 (0.21), residues: 1489 helix: -0.33 (0.19), residues: 785 sheet: -1.52 (0.45), residues: 136 loop : -1.92 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 367 TYR 0.033 0.002 TYR K 107 PHE 0.022 0.001 PHE T 616 TRP 0.010 0.001 TRP T 531 HIS 0.004 0.001 HIS K 329 Details of bonding type rmsd covalent geometry : bond 0.00318 (12121) covalent geometry : angle 0.60462 (16456) hydrogen bonds : bond 0.03369 ( 509) hydrogen bonds : angle 4.69011 ( 1449) metal coordination : bond 0.00261 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: K 130 MET cc_start: 0.8312 (mmm) cc_final: 0.7903 (mmp) REVERT: K 174 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7433 (p) REVERT: T 137 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7427 (mp) REVERT: T 616 PHE cc_start: 0.6344 (m-80) cc_final: 0.6078 (m-80) outliers start: 19 outliers final: 11 residues processed: 137 average time/residue: 0.0992 time to fit residues: 20.2654 Evaluate side-chains 130 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 224 ASN K 186 HIS ** K 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144473 restraints weight = 16367.781| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.71 r_work: 0.3754 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12127 Z= 0.209 Angle : 0.651 11.026 16456 Z= 0.323 Chirality : 0.045 0.168 1909 Planarity : 0.005 0.058 2093 Dihedral : 5.302 47.599 1615 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.98 % Allowed : 14.75 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.66 (0.22), residues: 1489 helix: -0.38 (0.18), residues: 802 sheet: -1.61 (0.45), residues: 136 loop : -1.91 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 367 TYR 0.031 0.002 TYR K 107 PHE 0.014 0.002 PHE T 616 TRP 0.013 0.002 TRP I 225 HIS 0.005 0.001 HIS I 397 Details of bonding type rmsd covalent geometry : bond 0.00511 (12121) covalent geometry : angle 0.65068 (16456) hydrogen bonds : bond 0.03551 ( 509) hydrogen bonds : angle 4.72147 ( 1449) metal coordination : bond 0.00578 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: I 203 ILE cc_start: 0.5728 (OUTLIER) cc_final: 0.5252 (mp) REVERT: I 488 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7688 (pp) REVERT: K 174 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7505 (p) REVERT: T 137 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7470 (mp) REVERT: T 305 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7744 (pp) REVERT: T 775 MET cc_start: 0.7474 (tpt) cc_final: 0.7250 (tpt) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 0.0941 time to fit residues: 19.4243 Evaluate side-chains 135 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 646 LEU Chi-restraints excluded: chain T residue 655 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.167388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146844 restraints weight = 16225.620| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.70 r_work: 0.3783 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12127 Z= 0.145 Angle : 0.592 11.559 16456 Z= 0.294 Chirality : 0.043 0.169 1909 Planarity : 0.005 0.057 2093 Dihedral : 5.049 43.423 1615 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.59 % Allowed : 15.44 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.33 (0.22), residues: 1489 helix: -0.12 (0.19), residues: 796 sheet: -1.42 (0.46), residues: 136 loop : -1.76 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 367 TYR 0.029 0.002 TYR K 107 PHE 0.011 0.001 PHE K 69 TRP 0.012 0.001 TRP I 225 HIS 0.004 0.001 HIS K 157 Details of bonding type rmsd covalent geometry : bond 0.00352 (12121) covalent geometry : angle 0.59214 (16456) hydrogen bonds : bond 0.03159 ( 509) hydrogen bonds : angle 4.47079 ( 1449) metal coordination : bond 0.00316 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 203 ILE cc_start: 0.5535 (OUTLIER) cc_final: 0.5090 (mp) REVERT: I 488 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (pp) REVERT: T 137 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7389 (mp) outliers start: 34 outliers final: 22 residues processed: 155 average time/residue: 0.0977 time to fit residues: 22.6963 Evaluate side-chains 143 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 486 MET Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 465 THR Chi-restraints excluded: chain T residue 618 GLU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145210 restraints weight = 16345.569| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.71 r_work: 0.3763 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12127 Z= 0.183 Angle : 0.633 11.938 16456 Z= 0.312 Chirality : 0.044 0.172 1909 Planarity : 0.005 0.056 2093 Dihedral : 5.102 42.116 1615 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.74 % Allowed : 16.65 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.30 (0.22), residues: 1489 helix: -0.12 (0.19), residues: 797 sheet: -1.32 (0.47), residues: 134 loop : -1.72 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 367 TYR 0.027 0.002 TYR K 107 PHE 0.012 0.001 PHE K 69 TRP 0.012 0.001 TRP I 225 HIS 0.005 0.001 HIS K 157 Details of bonding type rmsd covalent geometry : bond 0.00447 (12121) covalent geometry : angle 0.63335 (16456) hydrogen bonds : bond 0.03279 ( 509) hydrogen bonds : angle 4.54584 ( 1449) metal coordination : bond 0.00477 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7906 (mtp) cc_final: 0.7695 (mtp) REVERT: I 203 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.5166 (mp) REVERT: I 488 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (pp) REVERT: T 12 LEU cc_start: 0.8070 (tp) cc_final: 0.7859 (tp) REVERT: T 137 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7400 (mp) outliers start: 36 outliers final: 26 residues processed: 147 average time/residue: 0.0944 time to fit residues: 21.0823 Evaluate side-chains 148 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 486 MET Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 186 HIS Chi-restraints excluded: chain K residue 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 422 CYS Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 465 THR Chi-restraints excluded: chain T residue 618 GLU Chi-restraints excluded: chain T residue 646 LEU Chi-restraints excluded: chain T residue 655 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 140 GLN ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 443 GLN ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.168431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147869 restraints weight = 16137.571| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.71 r_work: 0.3792 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12127 Z= 0.137 Angle : 0.592 12.047 16456 Z= 0.293 Chirality : 0.043 0.168 1909 Planarity : 0.005 0.057 2093 Dihedral : 4.876 37.863 1615 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.51 % Allowed : 16.96 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.00 (0.22), residues: 1489 helix: 0.16 (0.19), residues: 789 sheet: -1.10 (0.48), residues: 133 loop : -1.66 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 367 TYR 0.029 0.002 TYR K 107 PHE 0.024 0.001 PHE K 60 TRP 0.014 0.001 TRP I 225 HIS 0.004 0.001 HIS T 598 Details of bonding type rmsd covalent geometry : bond 0.00337 (12121) covalent geometry : angle 0.59248 (16456) hydrogen bonds : bond 0.02999 ( 509) hydrogen bonds : angle 4.32906 ( 1449) metal coordination : bond 0.00258 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 203 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.5132 (mp) REVERT: T 137 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 33 outliers final: 24 residues processed: 147 average time/residue: 0.0951 time to fit residues: 21.1995 Evaluate side-chains 147 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 186 HIS Chi-restraints excluded: chain K residue 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 395 VAL Chi-restraints excluded: chain T residue 422 CYS Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 618 GLU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 140 GLN ** K 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.164928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144067 restraints weight = 16234.692| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.72 r_work: 0.3752 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12127 Z= 0.216 Angle : 0.665 11.876 16456 Z= 0.327 Chirality : 0.046 0.329 1909 Planarity : 0.005 0.056 2093 Dihedral : 5.092 38.824 1615 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.51 % Allowed : 17.64 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.21 (0.22), residues: 1489 helix: -0.03 (0.19), residues: 789 sheet: -1.39 (0.47), residues: 136 loop : -1.65 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 367 TYR 0.027 0.002 TYR K 107 PHE 0.014 0.002 PHE K 69 TRP 0.015 0.002 TRP I 225 HIS 0.006 0.001 HIS K 157 Details of bonding type rmsd covalent geometry : bond 0.00531 (12121) covalent geometry : angle 0.66509 (16456) hydrogen bonds : bond 0.03378 ( 509) hydrogen bonds : angle 4.57931 ( 1449) metal coordination : bond 0.00562 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7910 (mtp) cc_final: 0.7659 (mtm) REVERT: I 203 ILE cc_start: 0.5622 (OUTLIER) cc_final: 0.5228 (mp) REVERT: T 137 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7432 (mp) outliers start: 33 outliers final: 29 residues processed: 141 average time/residue: 0.0886 time to fit residues: 18.7624 Evaluate side-chains 144 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 186 HIS Chi-restraints excluded: chain K residue 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 395 VAL Chi-restraints excluded: chain T residue 422 CYS Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 465 THR Chi-restraints excluded: chain T residue 551 LEU Chi-restraints excluded: chain T residue 618 GLU Chi-restraints excluded: chain T residue 646 LEU Chi-restraints excluded: chain T residue 655 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.170107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.149719 restraints weight = 15964.659| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.71 r_work: 0.3816 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12127 Z= 0.120 Angle : 0.596 12.670 16456 Z= 0.291 Chirality : 0.042 0.215 1909 Planarity : 0.005 0.057 2093 Dihedral : 4.756 33.830 1615 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.05 % Allowed : 17.79 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.77 (0.22), residues: 1489 helix: 0.36 (0.19), residues: 783 sheet: -1.29 (0.50), residues: 120 loop : -1.46 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 367 TYR 0.031 0.001 TYR K 107 PHE 0.010 0.001 PHE T 616 TRP 0.014 0.001 TRP T 531 HIS 0.005 0.001 HIS T 598 Details of bonding type rmsd covalent geometry : bond 0.00294 (12121) covalent geometry : angle 0.59599 (16456) hydrogen bonds : bond 0.02897 ( 509) hydrogen bonds : angle 4.21954 ( 1449) metal coordination : bond 0.00215 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 96 VAL cc_start: 0.6154 (p) cc_final: 0.5930 (p) REVERT: I 203 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5122 (mp) REVERT: K 260 ASN cc_start: 0.5835 (OUTLIER) cc_final: 0.5182 (t0) REVERT: T 8 LEU cc_start: 0.7563 (mt) cc_final: 0.7316 (tp) REVERT: T 137 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7349 (mp) REVERT: T 443 GLN cc_start: 0.7432 (tt0) cc_final: 0.7209 (tt0) REVERT: T 616 PHE cc_start: 0.6166 (m-80) cc_final: 0.5959 (m-80) outliers start: 27 outliers final: 21 residues processed: 144 average time/residue: 0.0841 time to fit residues: 18.5136 Evaluate side-chains 144 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 375 HIS Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 186 HIS Chi-restraints excluded: chain K residue 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 302 PHE Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 395 VAL Chi-restraints excluded: chain T residue 465 THR Chi-restraints excluded: chain T residue 618 GLU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 116 HIS ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.171391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.150887 restraints weight = 16165.131| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.73 r_work: 0.3827 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12127 Z= 0.114 Angle : 0.587 13.390 16456 Z= 0.286 Chirality : 0.042 0.197 1909 Planarity : 0.005 0.057 2093 Dihedral : 4.567 29.254 1615 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.52 % Allowed : 18.40 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.57 (0.22), residues: 1489 helix: 0.53 (0.20), residues: 782 sheet: -1.13 (0.50), residues: 120 loop : -1.41 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 367 TYR 0.033 0.002 TYR K 107 PHE 0.010 0.001 PHE K 337 TRP 0.015 0.001 TRP T 531 HIS 0.004 0.001 HIS T 598 Details of bonding type rmsd covalent geometry : bond 0.00278 (12121) covalent geometry : angle 0.58744 (16456) hydrogen bonds : bond 0.02820 ( 509) hydrogen bonds : angle 4.09917 ( 1449) metal coordination : bond 0.00145 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: I 203 ILE cc_start: 0.5469 (OUTLIER) cc_final: 0.5062 (mp) REVERT: K 260 ASN cc_start: 0.5770 (OUTLIER) cc_final: 0.5036 (t0) REVERT: T 137 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7324 (mp) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.0766 time to fit residues: 16.8180 Evaluate side-chains 137 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 375 HIS Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 302 PHE Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 137 LEU Chi-restraints excluded: chain T residue 465 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 GLN ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.170520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.149925 restraints weight = 16142.482| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.72 r_work: 0.3815 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12127 Z= 0.130 Angle : 0.598 13.387 16456 Z= 0.291 Chirality : 0.043 0.330 1909 Planarity : 0.004 0.056 2093 Dihedral : 4.596 28.806 1615 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.90 % Allowed : 18.56 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.57 (0.22), residues: 1489 helix: 0.52 (0.20), residues: 782 sheet: -1.10 (0.50), residues: 120 loop : -1.37 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 367 TYR 0.029 0.001 TYR K 107 PHE 0.022 0.001 PHE T 616 TRP 0.014 0.001 TRP I 225 HIS 0.004 0.001 HIS T 598 Details of bonding type rmsd covalent geometry : bond 0.00321 (12121) covalent geometry : angle 0.59785 (16456) hydrogen bonds : bond 0.02862 ( 509) hydrogen bonds : angle 4.11480 ( 1449) metal coordination : bond 0.00248 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.35 seconds wall clock time: 45 minutes 45.95 seconds (2745.95 seconds total)