Starting phenix.real_space_refine on Wed Mar 4 06:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrj_14916/03_2026/7zrj_14916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrj_14916/03_2026/7zrj_14916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrj_14916/03_2026/7zrj_14916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrj_14916/03_2026/7zrj_14916.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrj_14916/03_2026/7zrj_14916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrj_14916/03_2026/7zrj_14916.cif" } resolution = 3.7 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 7 8.98 5 P 5 5.49 5 S 62 5.16 5 C 7120 2.51 5 N 1821 2.21 5 O 1994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11009 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5016 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 206 Unusual residues: {' K': 6, 'CDL': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.19 Number of scatterers: 11009 At special positions: 0 Unit cell: (98.164, 112.332, 153.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 7 19.00 S 62 16.00 P 5 15.00 O 1994 8.00 N 1821 7.00 C 7120 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: 0.95 Conformation dependent library (CDL) restraints added in 466.6 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 62.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.624A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.898A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 82 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.742A pdb=" N GLN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 removed outlier: 3.576A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.791A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.606A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.838A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 305 removed outlier: 4.023A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.914A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.533A pdb=" N PHE A 354 " --> pdb=" O HIS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.788A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 removed outlier: 3.688A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 435 removed outlier: 4.650A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.797A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.064A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 510 removed outlier: 4.020A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 538 Processing helix chain 'A' and resid 543 through 549 removed outlier: 4.165A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.535A pdb=" N TRP C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.910A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 5 through 25 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 33 through 56 removed outlier: 4.200A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 99 removed outlier: 4.108A pdb=" N GLY B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 215 through 246 removed outlier: 4.403A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.718A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 272 through 285 removed outlier: 5.977A pdb=" N GLY B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.578A pdb=" N GLY B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.143A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.621A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 605 removed outlier: 4.135A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.782A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 661 removed outlier: 4.372A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 680 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.874A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 155 removed outlier: 6.103A pdb=" N VAL B 153 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 163 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 155 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 161 " --> pdb=" O GLU B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 removed outlier: 6.670A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 393 through 396 removed outlier: 6.262A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 435 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 438 " --> pdb=" O GLU B 435 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1869 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: 1.82 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1859 1.32 - 1.45: 2669 1.45 - 1.57: 6548 1.57 - 1.69: 12 1.69 - 1.82: 112 Bond restraints: 11200 Sorted by residual: bond pdb=" OA3 CDL A 607 " pdb=" PA1 CDL A 607 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.20e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.95e+00 bond pdb=" N ASP C 111 " pdb=" CA ASP C 111 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.86e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.27e+00 bond pdb=" OB3 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 ... (remaining 11195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 14796 2.14 - 4.29: 313 4.29 - 6.43: 63 6.43 - 8.57: 19 8.57 - 10.72: 6 Bond angle restraints: 15197 Sorted by residual: angle pdb=" C GLY A 83 " pdb=" N GLN A 84 " pdb=" CA GLN A 84 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" N GLU B 544 " pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " ideal model delta sigma weight residual 110.28 117.15 -6.87 1.55e+00 4.16e-01 1.96e+01 angle pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " pdb=" CG GLU B 544 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB MET A 227 " pdb=" CG MET A 227 " pdb=" SD MET A 227 " ideal model delta sigma weight residual 112.70 123.42 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.24 -6.34 1.80e+00 3.09e-01 1.24e+01 ... (remaining 15192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5880 17.26 - 34.51: 636 34.51 - 51.77: 156 51.77 - 69.02: 45 69.02 - 86.28: 15 Dihedral angle restraints: 6732 sinusoidal: 2629 harmonic: 4103 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE A 373 " pdb=" C PHE A 373 " pdb=" N GLY A 374 " pdb=" CA GLY A 374 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ILE B 656 " pdb=" C ILE B 656 " pdb=" N TYR B 657 " pdb=" CA TYR B 657 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 6729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1433 0.058 - 0.116: 332 0.116 - 0.174: 39 0.174 - 0.233: 3 0.233 - 0.291: 3 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE B 386 " pdb=" CA ILE B 386 " pdb=" CG1 ILE B 386 " pdb=" CG2 ILE B 386 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL C 175 " pdb=" CA VAL C 175 " pdb=" CG1 VAL C 175 " pdb=" CG2 VAL C 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1807 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 153 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" CD GLU C 153 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU C 153 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 116 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 117 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO C 134 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.031 5.00e-02 4.00e+02 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.77: 2044 2.77 - 3.36: 12829 3.36 - 3.96: 21825 3.96 - 4.55: 30073 4.55 - 5.14: 44847 Nonbonded interactions: 111618 Sorted by model distance: nonbonded pdb=" O ASP C 111 " pdb=" OD1 ASP C 111 " model vdw 2.179 3.040 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.205 3.040 nonbonded pdb=" O THR A 248 " pdb=" OG1 THR A 251 " model vdw 2.268 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.294 3.040 nonbonded pdb=" O PRO C 23 " pdb=" OG1 THR C 27 " model vdw 2.296 3.040 ... (remaining 111613 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 group one per residue 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: 1.030 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.004 0.043 11200 Z= 0.199 Angle : 0.804 10.716 15197 Z= 0.406 Chirality : 0.049 0.291 1810 Planarity : 0.005 0.057 1908 Dihedral : 16.082 86.276 4096 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1438 helix: -0.15 (0.17), residues: 859 sheet: -1.55 (0.79), residues: 35 loop : -1.80 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 55 TYR 0.029 0.002 TYR A 381 PHE 0.030 0.002 PHE C 34 TRP 0.016 0.001 TRP A 115 HIS 0.002 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00391 (11200) covalent geometry : angle 0.80405 (15197) hydrogen bonds : bond 0.10175 ( 637) hydrogen bonds : angle 5.27452 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.248 Fit side-chains REVERT: A 176 TRP cc_start: 0.7393 (m100) cc_final: 0.7135 (m100) REVERT: A 412 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6656 (mmt180) REVERT: B 303 VAL cc_start: 0.8514 (t) cc_final: 0.8105 (t) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0790 time to fit residues: 19.7188 Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 466 ASN A 467 ASN A 513 GLN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083976 restraints weight = 21370.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086062 restraints weight = 12119.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087262 restraints weight = 8490.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087797 restraints weight = 6903.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088584 restraints weight = 6205.757| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11200 Z= 0.291 Angle : 0.721 10.089 15197 Z= 0.365 Chirality : 0.046 0.156 1810 Planarity : 0.005 0.044 1908 Dihedral : 11.212 83.049 1714 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.85 % Allowed : 10.57 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1438 helix: 0.51 (0.18), residues: 857 sheet: -1.66 (0.71), residues: 49 loop : -1.73 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 68 TYR 0.025 0.003 TYR A 458 PHE 0.027 0.002 PHE A 373 TRP 0.009 0.002 TRP B 655 HIS 0.005 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00682 (11200) covalent geometry : angle 0.72079 (15197) hydrogen bonds : bond 0.04711 ( 637) hydrogen bonds : angle 4.85796 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.380 Fit side-chains REVERT: A 176 TRP cc_start: 0.7645 (m100) cc_final: 0.7338 (m100) REVERT: A 187 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8962 (mm) REVERT: A 445 MET cc_start: 0.8165 (mmt) cc_final: 0.7090 (mmt) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.0822 time to fit residues: 17.2950 Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088555 restraints weight = 21381.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.090781 restraints weight = 11733.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092152 restraints weight = 8038.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092843 restraints weight = 6389.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093510 restraints weight = 5619.146| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11200 Z= 0.121 Angle : 0.562 7.791 15197 Z= 0.283 Chirality : 0.041 0.144 1810 Planarity : 0.004 0.044 1908 Dihedral : 10.625 83.778 1714 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.67 % Allowed : 12.16 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1438 helix: 0.97 (0.18), residues: 865 sheet: -1.26 (0.71), residues: 49 loop : -1.59 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.021 0.002 TYR A 381 PHE 0.014 0.001 PHE B 173 TRP 0.016 0.001 TRP A 115 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00268 (11200) covalent geometry : angle 0.56179 (15197) hydrogen bonds : bond 0.03771 ( 637) hydrogen bonds : angle 4.41428 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7492 (m100) cc_final: 0.7201 (m100) REVERT: A 445 MET cc_start: 0.8179 (mmt) cc_final: 0.7362 (mmt) REVERT: B 469 MET cc_start: 0.7384 (ttt) cc_final: 0.7024 (mtp) outliers start: 19 outliers final: 9 residues processed: 146 average time/residue: 0.0857 time to fit residues: 18.7988 Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.090167 restraints weight = 21336.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092432 restraints weight = 11587.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093890 restraints weight = 7845.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094575 restraints weight = 6174.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095016 restraints weight = 5408.687| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11200 Z= 0.107 Angle : 0.537 6.125 15197 Z= 0.271 Chirality : 0.040 0.143 1810 Planarity : 0.004 0.043 1908 Dihedral : 9.925 83.933 1714 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.94 % Allowed : 15.15 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1438 helix: 1.19 (0.18), residues: 859 sheet: -1.01 (0.71), residues: 49 loop : -1.45 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.021 0.002 TYR A 381 PHE 0.012 0.001 PHE B 173 TRP 0.009 0.001 TRP A 115 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00231 (11200) covalent geometry : angle 0.53748 (15197) hydrogen bonds : bond 0.03462 ( 637) hydrogen bonds : angle 4.24992 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7515 (m100) cc_final: 0.7265 (m100) REVERT: A 445 MET cc_start: 0.8136 (mmt) cc_final: 0.7270 (mmt) REVERT: B 406 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 469 MET cc_start: 0.7204 (ttt) cc_final: 0.7000 (mtp) outliers start: 22 outliers final: 11 residues processed: 148 average time/residue: 0.0814 time to fit residues: 18.4464 Evaluate side-chains 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091191 restraints weight = 21310.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090906 restraints weight = 13532.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091148 restraints weight = 11822.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091136 restraints weight = 10749.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091292 restraints weight = 10444.747| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11200 Z= 0.165 Angle : 0.587 8.799 15197 Z= 0.294 Chirality : 0.042 0.243 1810 Planarity : 0.004 0.042 1908 Dihedral : 9.741 80.883 1714 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.38 % Allowed : 15.68 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1438 helix: 1.17 (0.18), residues: 859 sheet: -0.84 (0.72), residues: 49 loop : -1.48 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.018 0.002 TYR A 381 PHE 0.016 0.001 PHE A 373 TRP 0.013 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00385 (11200) covalent geometry : angle 0.58679 (15197) hydrogen bonds : bond 0.03750 ( 637) hydrogen bonds : angle 4.33591 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7554 (m100) cc_final: 0.7311 (m100) REVERT: A 256 MET cc_start: 0.8260 (mtt) cc_final: 0.7962 (mtt) REVERT: A 445 MET cc_start: 0.8442 (mmt) cc_final: 0.7675 (mmt) REVERT: C 94 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9061 (tt) REVERT: B 469 MET cc_start: 0.7376 (ttt) cc_final: 0.7138 (mtp) outliers start: 27 outliers final: 13 residues processed: 139 average time/residue: 0.0834 time to fit residues: 17.8090 Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 603 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 0.0270 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN C 157 GLN B 603 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.120687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093544 restraints weight = 21277.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092993 restraints weight = 13893.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093199 restraints weight = 13010.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093307 restraints weight = 11005.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093476 restraints weight = 10595.805| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11200 Z= 0.111 Angle : 0.555 8.559 15197 Z= 0.277 Chirality : 0.040 0.142 1810 Planarity : 0.004 0.043 1908 Dihedral : 9.284 81.441 1714 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.59 % Allowed : 16.48 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1438 helix: 1.25 (0.18), residues: 868 sheet: -0.69 (0.73), residues: 49 loop : -1.42 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.021 0.001 TYR A 381 PHE 0.012 0.001 PHE B 173 TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00247 (11200) covalent geometry : angle 0.55491 (15197) hydrogen bonds : bond 0.03479 ( 637) hydrogen bonds : angle 4.20871 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.387 Fit side-chains REVERT: A 176 TRP cc_start: 0.7520 (m100) cc_final: 0.7290 (m100) REVERT: A 187 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8891 (mm) REVERT: A 256 MET cc_start: 0.8179 (mtt) cc_final: 0.7852 (mtt) REVERT: A 397 MET cc_start: 0.7999 (mtt) cc_final: 0.7497 (mtt) REVERT: A 445 MET cc_start: 0.8383 (mmt) cc_final: 0.7651 (mmt) REVERT: B 518 ASP cc_start: 0.6299 (p0) cc_final: 0.6021 (p0) outliers start: 18 outliers final: 10 residues processed: 139 average time/residue: 0.0881 time to fit residues: 18.5575 Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 587 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 100 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090595 restraints weight = 21228.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.090776 restraints weight = 13653.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.091077 restraints weight = 10910.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091489 restraints weight = 10423.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091530 restraints weight = 9292.043| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11200 Z= 0.172 Angle : 0.602 10.013 15197 Z= 0.301 Chirality : 0.042 0.144 1810 Planarity : 0.004 0.042 1908 Dihedral : 9.302 78.357 1714 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.38 % Allowed : 16.39 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1438 helix: 1.21 (0.18), residues: 857 sheet: -0.63 (0.74), residues: 49 loop : -1.46 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.019 0.002 TYR A 381 PHE 0.016 0.001 PHE A 373 TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00403 (11200) covalent geometry : angle 0.60184 (15197) hydrogen bonds : bond 0.03750 ( 637) hydrogen bonds : angle 4.32180 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7554 (m100) cc_final: 0.7320 (m100) REVERT: A 187 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 256 MET cc_start: 0.8280 (mtt) cc_final: 0.7937 (mtt) REVERT: A 397 MET cc_start: 0.8120 (mtt) cc_final: 0.7716 (mtt) REVERT: A 445 MET cc_start: 0.8509 (mmt) cc_final: 0.7621 (mmt) REVERT: B 383 MET cc_start: 0.6138 (ttt) cc_final: 0.4947 (tmm) outliers start: 27 outliers final: 15 residues processed: 136 average time/residue: 0.0867 time to fit residues: 17.9515 Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 587 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 3 optimal weight: 0.0470 chunk 125 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093342 restraints weight = 21220.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092844 restraints weight = 16107.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092955 restraints weight = 13779.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093045 restraints weight = 12822.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093542 restraints weight = 11493.256| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11200 Z= 0.125 Angle : 0.581 12.327 15197 Z= 0.287 Chirality : 0.041 0.154 1810 Planarity : 0.004 0.042 1908 Dihedral : 9.096 78.465 1714 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.94 % Allowed : 16.48 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1438 helix: 1.20 (0.18), residues: 864 sheet: -0.42 (0.75), residues: 49 loop : -1.40 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.021 0.001 TYR A 381 PHE 0.013 0.001 PHE B 173 TRP 0.010 0.001 TRP B 31 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00286 (11200) covalent geometry : angle 0.58105 (15197) hydrogen bonds : bond 0.03537 ( 637) hydrogen bonds : angle 4.24902 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7502 (m100) cc_final: 0.7290 (m100) REVERT: A 187 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8855 (mm) REVERT: A 445 MET cc_start: 0.8535 (mmt) cc_final: 0.7736 (mmt) REVERT: B 31 TRP cc_start: 0.7618 (p-90) cc_final: 0.7305 (p-90) REVERT: B 383 MET cc_start: 0.6034 (ttt) cc_final: 0.5022 (tmm) REVERT: B 518 ASP cc_start: 0.6133 (p0) cc_final: 0.5838 (p0) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.0880 time to fit residues: 17.6371 Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 603 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 0.0470 chunk 62 optimal weight: 0.0980 chunk 135 optimal weight: 4.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091836 restraints weight = 21185.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091518 restraints weight = 14234.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091971 restraints weight = 13117.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091982 restraints weight = 10861.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092278 restraints weight = 10460.766| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11200 Z= 0.141 Angle : 0.595 12.435 15197 Z= 0.293 Chirality : 0.041 0.145 1810 Planarity : 0.004 0.042 1908 Dihedral : 9.081 77.365 1714 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.94 % Allowed : 17.00 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.22), residues: 1438 helix: 1.17 (0.18), residues: 862 sheet: -0.35 (0.76), residues: 49 loop : -1.40 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.020 0.002 TYR A 381 PHE 0.017 0.001 PHE B 78 TRP 0.014 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00328 (11200) covalent geometry : angle 0.59479 (15197) hydrogen bonds : bond 0.03602 ( 637) hydrogen bonds : angle 4.25507 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8491 (mp) cc_final: 0.8265 (mp) REVERT: A 176 TRP cc_start: 0.7497 (m100) cc_final: 0.7282 (m100) REVERT: A 187 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (mm) REVERT: A 445 MET cc_start: 0.8506 (mmt) cc_final: 0.7742 (mmt) REVERT: B 383 MET cc_start: 0.6190 (ttt) cc_final: 0.5120 (tmm) REVERT: B 518 ASP cc_start: 0.6291 (p0) cc_final: 0.5999 (p0) outliers start: 22 outliers final: 18 residues processed: 131 average time/residue: 0.0876 time to fit residues: 17.4726 Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 134 optimal weight: 0.1980 chunk 113 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094405 restraints weight = 21241.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094195 restraints weight = 13132.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094675 restraints weight = 12692.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094794 restraints weight = 10792.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095021 restraints weight = 10173.078| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11200 Z= 0.110 Angle : 0.577 12.212 15197 Z= 0.284 Chirality : 0.041 0.142 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.801 78.145 1714 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.59 % Allowed : 17.27 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1438 helix: 1.22 (0.18), residues: 863 sheet: -0.22 (0.77), residues: 49 loop : -1.33 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.022 0.001 TYR A 381 PHE 0.015 0.001 PHE B 78 TRP 0.011 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00241 (11200) covalent geometry : angle 0.57731 (15197) hydrogen bonds : bond 0.03464 ( 637) hydrogen bonds : angle 4.16879 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8360 (m-30) cc_final: 0.8140 (m-30) REVERT: A 170 LEU cc_start: 0.8401 (mp) cc_final: 0.8169 (mp) REVERT: A 187 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 445 MET cc_start: 0.8409 (mmt) cc_final: 0.7662 (mmt) REVERT: B 383 MET cc_start: 0.6276 (ttt) cc_final: 0.5210 (tmm) REVERT: B 518 ASP cc_start: 0.6288 (p0) cc_final: 0.6011 (p0) outliers start: 18 outliers final: 16 residues processed: 142 average time/residue: 0.0914 time to fit residues: 19.6455 Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 603 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.121419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094349 restraints weight = 21190.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093792 restraints weight = 13856.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094283 restraints weight = 12526.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094346 restraints weight = 10595.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094501 restraints weight = 10247.301| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11200 Z= 0.115 Angle : 0.581 11.500 15197 Z= 0.286 Chirality : 0.041 0.170 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.655 77.547 1714 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.94 % Allowed : 17.36 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1438 helix: 1.21 (0.18), residues: 864 sheet: -0.28 (0.75), residues: 49 loop : -1.32 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.021 0.001 TYR A 381 PHE 0.023 0.001 PHE B 78 TRP 0.010 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00260 (11200) covalent geometry : angle 0.58128 (15197) hydrogen bonds : bond 0.03445 ( 637) hydrogen bonds : angle 4.20844 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.29 seconds wall clock time: 28 minutes 46.09 seconds (1726.09 seconds total)