Starting phenix.real_space_refine on Mon Dec 30 00:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uib_42291/12_2024/8uib_42291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uib_42291/12_2024/8uib_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_42291/12_2024/8uib_42291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uib_42291/12_2024/8uib_42291.map" model { file = "/net/cci-nas-00/data/ceres_data/8uib_42291/12_2024/8uib_42291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uib_42291/12_2024/8uib_42291.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 1, 'ARG: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: 7.29, per 1000 atoms: 0.61 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.70 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: 3.64 Time building geometry restraints manager: 3.40 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: 2.190 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- 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 12121 Z= 0.414 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 : 10.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP I 225 HIS 0.008 0.001 HIS K 137 PHE 0.064 0.003 PHE T 616 TYR 0.029 0.003 TYR K 107 ARG 0.011 0.001 ARG T 367 *********************** 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 : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 167 average time/residue: 0.2538 time to fit residues: 60.8697 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 : 1.438 ------------------------------------------------------------------------------- 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 128 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.0170 chunk 77 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 226 HIS T 91 GLN ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12121 Z= 0.237 Angle : 0.646 11.431 16456 Z= 0.324 Chirality : 0.044 0.183 1909 Planarity : 0.005 0.061 2093 Dihedral : 5.849 53.020 1619 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.68 % Allowed : 8.59 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), residues: 1489 helix: -0.74 (0.18), residues: 792 sheet: -1.76 (0.43), residues: 140 loop : -2.06 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 123 HIS 0.003 0.001 HIS K 157 PHE 0.032 0.002 PHE T 616 TYR 0.047 0.002 TYR K 107 ARG 0.006 0.000 ARG T 562 *********************** 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 146 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: K 107 TYR cc_start: 0.6609 (t80) cc_final: 0.6321 (t80) REVERT: K 350 MET cc_start: 0.8303 (mmt) cc_final: 0.8037 (mmt) REVERT: T 91 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: T 174 LEU cc_start: 0.7519 (tp) cc_final: 0.7295 (tp) REVERT: T 775 MET cc_start: 0.7549 (tpt) cc_final: 0.7233 (tpt) outliers start: 9 outliers final: 6 residues processed: 140 average time/residue: 0.2375 time to fit residues: 49.8070 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 : 1.405 ------------------------------------------------------------------------------- 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 76 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 224 ASN ** K 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12121 Z= 0.318 Angle : 0.661 10.949 16456 Z= 0.327 Chirality : 0.045 0.178 1909 Planarity : 0.005 0.059 2093 Dihedral : 5.654 50.923 1619 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.14 % Allowed : 12.55 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1489 helix: -0.54 (0.18), residues: 796 sheet: -1.61 (0.45), residues: 136 loop : -1.95 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 237 HIS 0.005 0.001 HIS K 157 PHE 0.016 0.002 PHE I 328 TYR 0.035 0.002 TYR K 107 ARG 0.004 0.000 ARG T 367 *********************** 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 143 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.417 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.2241 time to fit residues: 44.8616 Evaluate side-chains 128 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE 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 281 LEU Chi-restraints excluded: chain K residue 340 TRP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12121 Z= 0.222 Angle : 0.607 11.734 16456 Z= 0.299 Chirality : 0.043 0.166 1909 Planarity : 0.005 0.058 2093 Dihedral : 5.197 47.902 1615 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.90 % Allowed : 13.99 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1489 helix: -0.21 (0.19), residues: 788 sheet: -1.45 (0.45), residues: 136 loop : -1.77 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 237 HIS 0.004 0.001 HIS I 375 PHE 0.013 0.001 PHE K 422 TYR 0.032 0.001 TYR K 107 ARG 0.004 0.000 ARG T 367 *********************** 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 156 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: I 203 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.4941 (mp) REVERT: K 130 MET cc_start: 0.8299 (mmm) cc_final: 0.8093 (mmp) REVERT: K 174 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7493 (p) REVERT: T 775 MET cc_start: 0.7514 (tpt) cc_final: 0.7301 (tpt) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 0.2411 time to fit residues: 51.7539 Evaluate side-chains 137 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE 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 330 SER 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 92 MET Chi-restraints excluded: chain K residue 108 ARG 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 K residue 437 MET Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0570 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 186 HIS ** K 346 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12121 Z= 0.311 Angle : 0.644 12.165 16456 Z= 0.317 Chirality : 0.045 0.197 1909 Planarity : 0.005 0.058 2093 Dihedral : 5.190 44.599 1615 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.28 % Allowed : 15.51 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.22), residues: 1489 helix: -0.23 (0.19), residues: 788 sheet: -1.46 (0.46), residues: 136 loop : -1.77 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 237 HIS 0.005 0.001 HIS K 157 PHE 0.013 0.002 PHE I 394 TYR 0.028 0.002 TYR K 107 ARG 0.004 0.000 ARG T 367 *********************** 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 161 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: I 108 MET cc_start: 0.7735 (mtp) cc_final: 0.7439 (mtp) REVERT: I 203 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.4933 (mp) REVERT: I 488 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7532 (pp) REVERT: K 328 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8260 (mm) REVERT: T 174 LEU cc_start: 0.7552 (tp) cc_final: 0.7301 (tp) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.2422 time to fit residues: 53.5827 Evaluate side-chains 140 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 260 ASN Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 124 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12121 Z= 0.279 Angle : 0.627 13.084 16456 Z= 0.308 Chirality : 0.044 0.173 1909 Planarity : 0.005 0.057 2093 Dihedral : 5.086 41.773 1615 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.66 % Allowed : 16.96 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1489 helix: -0.12 (0.19), residues: 787 sheet: -1.34 (0.47), residues: 135 loop : -1.74 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 237 HIS 0.004 0.001 HIS K 157 PHE 0.015 0.001 PHE K 422 TYR 0.029 0.002 TYR K 107 ARG 0.004 0.000 ARG T 367 *********************** 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 167 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7725 (mtp) cc_final: 0.7359 (mtm) REVERT: I 203 ILE cc_start: 0.5292 (OUTLIER) cc_final: 0.4956 (mp) REVERT: I 488 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7566 (pp) REVERT: K 328 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8230 (mm) REVERT: T 174 LEU cc_start: 0.7577 (tp) cc_final: 0.7271 (tp) outliers start: 35 outliers final: 26 residues processed: 155 average time/residue: 0.2257 time to fit residues: 52.3810 Evaluate side-chains 152 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 92 MET Chi-restraints excluded: chain K residue 108 ARG 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 328 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 327 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12121 Z= 0.187 Angle : 0.580 12.567 16456 Z= 0.285 Chirality : 0.042 0.170 1909 Planarity : 0.005 0.059 2093 Dihedral : 4.785 36.783 1615 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.43 % Allowed : 16.50 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1489 helix: 0.23 (0.19), residues: 783 sheet: -0.99 (0.48), residues: 133 loop : -1.63 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 531 HIS 0.004 0.001 HIS T 598 PHE 0.010 0.001 PHE T 616 TYR 0.029 0.001 TYR K 107 ARG 0.004 0.000 ARG T 367 *********************** 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 161 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7629 (mtp) cc_final: 0.7330 (mtm) REVERT: I 203 ILE cc_start: 0.5263 (OUTLIER) cc_final: 0.4847 (mp) REVERT: I 488 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7534 (pp) REVERT: K 328 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (mm) REVERT: T 174 LEU cc_start: 0.7521 (tp) cc_final: 0.7234 (tp) outliers start: 32 outliers final: 24 residues processed: 149 average time/residue: 0.2302 time to fit residues: 51.5808 Evaluate side-chains 148 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 420 VAL 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 92 MET Chi-restraints excluded: chain K residue 108 ARG 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 328 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 465 THR Chi-restraints excluded: chain T residue 569 MET 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 58 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 140 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12121 Z= 0.258 Angle : 0.622 14.172 16456 Z= 0.305 Chirality : 0.043 0.167 1909 Planarity : 0.005 0.058 2093 Dihedral : 4.840 35.794 1615 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.28 % Allowed : 17.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1489 helix: 0.25 (0.19), residues: 778 sheet: -0.98 (0.48), residues: 133 loop : -1.57 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 237 HIS 0.004 0.001 HIS K 157 PHE 0.021 0.001 PHE T 616 TYR 0.027 0.002 TYR K 107 ARG 0.004 0.000 ARG T 367 *********************** 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 151 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7611 (mtp) cc_final: 0.7292 (mtm) REVERT: I 203 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.4928 (mp) REVERT: I 488 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7499 (pp) REVERT: K 328 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8222 (mm) REVERT: T 174 LEU cc_start: 0.7578 (tp) cc_final: 0.7271 (tp) outliers start: 30 outliers final: 23 residues processed: 142 average time/residue: 0.2392 time to fit residues: 51.1450 Evaluate side-chains 143 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 113 ILE 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 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 260 ASN Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 436 LEU Chi-restraints excluded: chain T residue 465 THR Chi-restraints excluded: chain T residue 569 MET Chi-restraints excluded: chain T residue 618 GLU Chi-restraints excluded: chain T residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 0.0470 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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** T 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12121 Z= 0.173 Angle : 0.578 14.060 16456 Z= 0.283 Chirality : 0.041 0.174 1909 Planarity : 0.004 0.058 2093 Dihedral : 4.567 30.847 1615 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.83 % Allowed : 17.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1489 helix: 0.55 (0.20), residues: 779 sheet: -0.71 (0.49), residues: 133 loop : -1.52 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 531 HIS 0.005 0.001 HIS T 598 PHE 0.009 0.001 PHE K 337 TYR 0.026 0.001 TYR K 107 ARG 0.003 0.000 ARG T 367 *********************** 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 156 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7474 (mtp) cc_final: 0.7128 (mtm) REVERT: I 203 ILE cc_start: 0.5214 (OUTLIER) cc_final: 0.4886 (mp) REVERT: K 260 ASN cc_start: 0.5447 (OUTLIER) cc_final: 0.4893 (t0) REVERT: K 328 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8170 (mm) REVERT: T 174 LEU cc_start: 0.7509 (tp) cc_final: 0.7233 (tp) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.1999 time to fit residues: 45.3616 Evaluate side-chains 135 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 260 ASN Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 422 CYS 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 88 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 224 ASN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12121 Z= 0.311 Angle : 0.659 14.639 16456 Z= 0.320 Chirality : 0.045 0.371 1909 Planarity : 0.005 0.057 2093 Dihedral : 4.815 33.085 1615 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.67 % Allowed : 18.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1489 helix: 0.26 (0.19), residues: 778 sheet: -0.90 (0.49), residues: 133 loop : -1.54 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 225 HIS 0.005 0.001 HIS I 397 PHE 0.020 0.002 PHE T 616 TYR 0.029 0.002 TYR K 107 ARG 0.005 0.000 ARG T 367 ********************** 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 141 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 MET cc_start: 0.7630 (mtp) cc_final: 0.7261 (mtm) REVERT: I 203 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.5034 (mp) REVERT: K 260 ASN cc_start: 0.5566 (OUTLIER) cc_final: 0.4963 (t0) REVERT: K 328 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (mm) outliers start: 22 outliers final: 18 residues processed: 137 average time/residue: 0.2065 time to fit residues: 43.8835 Evaluate side-chains 135 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 330 SER Chi-restraints excluded: chain I residue 375 HIS 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 328 LEU Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 422 CYS 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 36 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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** ** 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 = 0.4150 r_free = 0.4150 target = 0.170760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150311 restraints weight = 15984.167| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.70 r_work: 0.3831 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12121 Z= 0.187 Angle : 0.605 14.519 16456 Z= 0.293 Chirality : 0.043 0.273 1909 Planarity : 0.004 0.057 2093 Dihedral : 4.647 31.172 1615 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.44 % Allowed : 18.56 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1489 helix: 0.46 (0.20), residues: 780 sheet: -1.12 (0.50), residues: 120 loop : -1.37 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 225 HIS 0.005 0.001 HIS T 598 PHE 0.010 0.001 PHE K 337 TYR 0.033 0.001 TYR K 107 ARG 0.003 0.000 ARG T 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.54 seconds wall clock time: 45 minutes 53.02 seconds (2753.02 seconds total)