Starting phenix.real_space_refine on Fri Jul 3 01:42:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrj_14916/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrj_14916/07_2026/7zrj_14916.map" } 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-6108/lib/python3.11/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: 2.17, per 1000 atoms: 0.20 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: 0.87 Conformation dependent library (CDL) restraints added in 604.4 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: 0.35 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: 2.04 Time building geometry restraints manager: 1.21 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: 5873 17.26 - 34.51: 619 34.51 - 51.77: 146 51.77 - 69.02: 40 69.02 - 86.28: 14 Dihedral angle restraints: 6692 sinusoidal: 2589 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 6689 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: 1.440 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 15.756 86.276 4056 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/Z covalent geometry : bond 0.00391 / 0.20 (11200) covalent geometry : angle 0.80405 / 0.41 (15197) hydrogen bonds : bond 0.10175 / 6.84 ( 637) hydrogen bonds : angle 5.27452 / 3.78 ( 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 : 0.419 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: 0.0847 time to fit residues: 21.2166 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 : 0.417 ------------------------------------------------------------------------------- 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... 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 = 0.3630 r_free = 0.3630 target = 0.115533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.083781 restraints weight = 21368.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085862 restraints weight = 12123.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086970 restraints weight = 8483.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.087901 restraints weight = 6926.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088211 restraints weight = 6066.822| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11200 Z= 0.293 Angle : 0.723 9.763 15197 Z= 0.367 Chirality : 0.046 0.166 1810 Planarity : 0.005 0.045 1908 Dihedral : 10.185 59.161 1674 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.23 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: -0.60 (0.22), residues: 1438 helix: 0.51 (0.18), residues: 856 sheet: -1.64 (0.71), residues: 49 loop : -1.74 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 212 TYR 0.026 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/Z covalent geometry : bond 0.00691 / 0.29 (11200) covalent geometry : angle 0.72293 / 0.37 (15197) hydrogen bonds : bond 0.04728 / 3.21 ( 637) hydrogen bonds : angle 4.86472 / 3.46 ( 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 : 0.414 Fit side-chains revert: symmetry clash REVERT: A 187 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8957 (mm) REVERT: A 445 MET cc_start: 0.8239 (mmt) cc_final: 0.7230 (mmt) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.0785 time to fit residues: 16.3431 Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 157 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 = 0.3676 r_free = 0.3676 target = 0.118639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.087443 restraints weight = 21379.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089682 restraints weight = 11357.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.090960 restraints weight = 7720.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091933 restraints weight = 6162.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092234 restraints weight = 5330.602| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1697 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= 0.136 Angle : 0.577 7.813 15197 Z= 0.291 Chirality : 0.041 0.145 1810 Planarity : 0.004 0.044 1908 Dihedral : 9.716 59.941 1674 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.59 % Allowed : 12.51 % Favored : 85.90 % 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: -0.11 (0.22), residues: 1438 helix: 0.91 (0.18), residues: 864 sheet: -1.26 (0.71), residues: 49 loop : -1.61 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.020 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/Z covalent geometry : bond 0.00308 / 0.14 (11200) covalent geometry : angle 0.57713 / 0.29 (15197) hydrogen bonds : bond 0.03885 / 2.67 ( 637) hydrogen bonds : angle 4.47808 / 3.16 ( 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 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8513 (mp) cc_final: 0.8135 (mp) REVERT: A 176 TRP cc_start: 0.7525 (m100) cc_final: 0.7240 (m100) REVERT: C 93 GLU cc_start: 0.8137 (tp30) cc_final: 0.7913 (tp30) REVERT: B 469 MET cc_start: 0.7390 (ttt) cc_final: 0.6995 (mtp) outliers start: 18 outliers final: 12 residues processed: 141 average time/residue: 0.0762 time to fit residues: 16.0806 Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 413 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 43 ILE 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 484 GLU 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: 1.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.120050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088954 restraints weight = 21363.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091208 restraints weight = 11618.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092639 restraints weight = 7897.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093233 restraints weight = 6218.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093242 restraints weight = 5522.147| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1732 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 : 0.540 6.424 15197 Z= 0.272 Chirality : 0.040 0.143 1810 Planarity : 0.004 0.043 1908 Dihedral : 9.078 59.898 1674 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.38 % Allowed : 14.27 % Favored : 83.35 % 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: 0.20 (0.22), residues: 1438 helix: 1.18 (0.18), residues: 860 sheet: -1.04 (0.71), residues: 49 loop : -1.51 (0.25), residues: 529 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 0.013 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/Z covalent geometry : bond 0.00256 / 0.11 (11200) covalent geometry : angle 0.54048 / 0.27 (15197) hydrogen bonds : bond 0.03541 / 2.43 ( 637) hydrogen bonds : angle 4.27225 / 3.00 ( 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 163 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7534 (m100) cc_final: 0.7292 (m100) REVERT: A 187 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8935 (mm) REVERT: A 445 MET cc_start: 0.8047 (mmt) cc_final: 0.7291 (mmt) REVERT: C 93 GLU cc_start: 0.8208 (tp30) cc_final: 0.7901 (tp30) REVERT: B 406 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: B 469 MET cc_start: 0.7243 (ttt) cc_final: 0.7003 (mtp) outliers start: 27 outliers final: 13 residues processed: 153 average time/residue: 0.0743 time to fit residues: 17.2821 Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 436 MET Chi-restraints excluded: chain C residue 34 PHE 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 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 526 LEU 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: 2.9990 chunk 61 optimal weight: 10.0000 chunk 54 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3711 r_free = 0.3711 target = 0.121020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092081 restraints weight = 21204.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092507 restraints weight = 12324.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093372 restraints weight = 9426.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093843 restraints weight = 7676.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093981 restraints weight = 6967.219| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11200 Z= 0.109 Angle : 0.543 8.773 15197 Z= 0.269 Chirality : 0.040 0.141 1810 Planarity : 0.004 0.043 1908 Dihedral : 8.578 59.622 1674 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.20 % Allowed : 14.98 % Favored : 82.82 % 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: 1.21 (0.18), residues: 868 sheet: -0.82 (0.72), residues: 49 loop : -1.40 (0.26), residues: 521 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 0.016 0.001 TRP A 115 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (11200) covalent geometry : angle 0.54265 / 0.27 (15197) hydrogen bonds : bond 0.03455 / 2.37 ( 637) hydrogen bonds : angle 4.18075 / 2.94 ( 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 153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7545 (m100) cc_final: 0.7275 (m100) REVERT: A 187 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8909 (mm) REVERT: A 256 MET cc_start: 0.8213 (mtt) cc_final: 0.7978 (mtt) REVERT: A 445 MET cc_start: 0.8031 (mmt) cc_final: 0.7505 (mmt) REVERT: C 128 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8865 (pp) REVERT: B 469 MET cc_start: 0.7384 (ttt) cc_final: 0.7180 (mtp) REVERT: B 518 ASP cc_start: 0.6390 (p0) cc_final: 0.6150 (p0) outliers start: 25 outliers final: 14 residues processed: 146 average time/residue: 0.0718 time to fit residues: 15.9018 Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 436 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 128 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 484 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 78 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3717 r_free = 0.3717 target = 0.121604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094553 restraints weight = 21217.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094280 restraints weight = 12998.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094606 restraints weight = 11577.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094552 restraints weight = 10269.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094727 restraints weight = 10163.826| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1879 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= 0.109 Angle : 0.548 8.430 15197 Z= 0.270 Chirality : 0.040 0.141 1810 Planarity : 0.004 0.043 1908 Dihedral : 8.140 58.739 1674 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.03 % Allowed : 15.59 % Favored : 82.38 % 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: 0.41 (0.23), residues: 1438 helix: 1.27 (0.18), residues: 867 sheet: -0.61 (0.73), residues: 49 loop : -1.35 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.012 0.001 PHE B 173 TRP 0.009 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11200) covalent geometry : angle 0.54805 / 0.27 (15197) hydrogen bonds : bond 0.03381 / 2.32 ( 637) hydrogen bonds : angle 4.14594 / 2.91 ( 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 153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8516 (mp) cc_final: 0.8183 (mp) REVERT: A 176 TRP cc_start: 0.7466 (m100) cc_final: 0.7200 (m100) REVERT: A 256 MET cc_start: 0.8198 (mtt) cc_final: 0.7873 (mtt) REVERT: A 445 MET cc_start: 0.7980 (mmt) cc_final: 0.7478 (mmt) REVERT: B 518 ASP cc_start: 0.6169 (p0) cc_final: 0.5908 (p0) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.0819 time to fit residues: 17.9122 Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 436 MET 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 266 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 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 = 0.3705 r_free = 0.3705 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093547 restraints weight = 21162.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093324 restraints weight = 19576.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094036 restraints weight = 15399.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094760 restraints weight = 12825.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094697 restraints weight = 11613.118| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11200 Z= 0.129 Angle : 0.568 10.318 15197 Z= 0.282 Chirality : 0.041 0.266 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.045 59.296 1674 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.29 % Allowed : 16.12 % 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: 0.38 (0.23), residues: 1438 helix: 1.23 (0.18), residues: 864 sheet: -0.54 (0.74), residues: 49 loop : -1.33 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.020 0.002 TYR A 381 PHE 0.012 0.001 PHE B 173 TRP 0.014 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11200) covalent geometry : angle 0.56773 / 0.28 (15197) hydrogen bonds : bond 0.03488 / 2.39 ( 637) hydrogen bonds : angle 4.19306 / 2.95 ( 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 147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8555 (mp) cc_final: 0.8192 (mp) REVERT: A 176 TRP cc_start: 0.7487 (m100) cc_final: 0.7220 (m100) REVERT: A 445 MET cc_start: 0.8204 (mmt) cc_final: 0.7606 (mmt) REVERT: B 383 MET cc_start: 0.5868 (ttt) cc_final: 0.4831 (tmm) REVERT: B 518 ASP cc_start: 0.5851 (p0) cc_final: 0.5571 (p0) outliers start: 26 outliers final: 18 residues processed: 141 average time/residue: 0.0795 time to fit residues: 16.9663 Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain C residue 157 GLN 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 266 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 484 GLU 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: 0.9980 chunk 125 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 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 = 0.3710 r_free = 0.3710 target = 0.121155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093890 restraints weight = 21230.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093652 restraints weight = 19058.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094375 restraints weight = 15114.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094635 restraints weight = 13667.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094826 restraints weight = 11740.019| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11200 Z= 0.117 Angle : 0.575 13.167 15197 Z= 0.281 Chirality : 0.041 0.174 1810 Planarity : 0.004 0.042 1908 Dihedral : 7.920 59.337 1674 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.03 % Allowed : 16.12 % Favored : 81.85 % 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: 0.44 (0.23), residues: 1438 helix: 1.27 (0.18), residues: 864 sheet: -0.39 (0.75), residues: 49 loop : -1.30 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.012 0.001 PHE B 173 TRP 0.010 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11200) covalent geometry : angle 0.57501 / 0.28 (15197) hydrogen bonds : bond 0.03432 / 2.35 ( 637) hydrogen bonds : angle 4.15664 / 2.92 ( 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 144 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8574 (mp) cc_final: 0.8192 (mp) REVERT: A 176 TRP cc_start: 0.7469 (m100) cc_final: 0.7207 (m100) REVERT: A 445 MET cc_start: 0.8230 (mmt) cc_final: 0.7593 (mmt) REVERT: B 383 MET cc_start: 0.5829 (ttt) cc_final: 0.4837 (tmm) REVERT: B 518 ASP cc_start: 0.5976 (p0) cc_final: 0.5708 (p0) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.0838 time to fit residues: 17.6454 Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 266 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 484 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 129 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 135 optimal weight: 0.2980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093138 restraints weight = 21347.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093162 restraints weight = 12967.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093529 restraints weight = 10857.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094241 restraints weight = 9392.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094259 restraints weight = 7806.933| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11200 Z= 0.109 Angle : 0.573 12.079 15197 Z= 0.283 Chirality : 0.040 0.149 1810 Planarity : 0.004 0.043 1908 Dihedral : 7.732 58.647 1674 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.67 % Allowed : 16.74 % 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: 0.47 (0.23), residues: 1438 helix: 1.28 (0.18), residues: 863 sheet: -0.30 (0.76), residues: 49 loop : -1.27 (0.26), residues: 526 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 0.010 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (11200) covalent geometry : angle 0.57342 / 0.28 (15197) hydrogen bonds : bond 0.03401 / 2.34 ( 637) hydrogen bonds : angle 4.13818 / 2.91 ( 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 144 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8585 (mp) cc_final: 0.8207 (mp) REVERT: A 176 TRP cc_start: 0.7500 (m100) cc_final: 0.7239 (m100) REVERT: A 445 MET cc_start: 0.8170 (mmt) cc_final: 0.7535 (mmt) REVERT: B 383 MET cc_start: 0.6407 (ttt) cc_final: 0.5224 (tmm) REVERT: B 518 ASP cc_start: 0.6354 (p0) cc_final: 0.6087 (p0) outliers start: 19 outliers final: 17 residues processed: 137 average time/residue: 0.0822 time to fit residues: 17.1669 Evaluate side-chains 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 266 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 484 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 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... A 465 ASN ** A 467 ASN ** 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 = 0.3732 r_free = 0.3732 target = 0.122193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094364 restraints weight = 21342.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094239 restraints weight = 12604.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095429 restraints weight = 9756.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095861 restraints weight = 8608.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095798 restraints weight = 7031.880| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11200 Z= 0.110 Angle : 0.582 11.079 15197 Z= 0.285 Chirality : 0.040 0.152 1810 Planarity : 0.004 0.043 1908 Dihedral : 7.581 59.579 1674 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.90 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: 0.49 (0.23), residues: 1438 helix: 1.29 (0.18), residues: 862 sheet: -0.31 (0.75), residues: 49 loop : -1.22 (0.26), residues: 527 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 C 34 TRP 0.014 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11200) covalent geometry : angle 0.58201 / 0.28 (15197) hydrogen bonds : bond 0.03399 / 2.35 ( 637) hydrogen bonds : angle 4.14061 / 2.91 ( 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 151 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7493 (m100) cc_final: 0.7229 (m100) REVERT: A 445 MET cc_start: 0.8132 (mmt) cc_final: 0.7466 (mmt) REVERT: B 383 MET cc_start: 0.6307 (ttt) cc_final: 0.5161 (tmm) REVERT: B 518 ASP cc_start: 0.6231 (p0) cc_final: 0.5951 (p0) outliers start: 22 outliers final: 19 residues processed: 143 average time/residue: 0.0809 time to fit residues: 17.6691 Evaluate side-chains 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 266 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 484 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 568 MET 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 83 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089260 restraints weight = 21338.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091469 restraints weight = 11607.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092898 restraints weight = 7915.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093575 restraints weight = 6292.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094108 restraints weight = 5557.099| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11200 Z= 0.137 Angle : 0.600 9.987 15197 Z= 0.294 Chirality : 0.041 0.170 1810 Planarity : 0.004 0.042 1908 Dihedral : 7.648 58.574 1674 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.03 % Allowed : 16.92 % 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: 0.45 (0.23), residues: 1438 helix: 1.26 (0.18), residues: 862 sheet: -0.28 (0.74), residues: 49 loop : -1.24 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.021 0.002 TYR A 381 PHE 0.013 0.001 PHE C 34 TRP 0.007 0.001 TRP A 115 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11200) covalent geometry : angle 0.60035 / 0.29 (15197) hydrogen bonds : bond 0.03574 / 2.46 ( 637) hydrogen bonds : angle 4.21736 / 2.96 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.94 seconds wall clock time: 27 minutes 18.57 seconds (1638.57 seconds total)