Starting phenix.real_space_refine on Sat Jul 20 17:30:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/07_2024/7zre_14912.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/07_2024/7zre_14912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/07_2024/7zre_14912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/07_2024/7zre_14912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/07_2024/7zre_14912.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/07_2024/7zre_14912.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 101 atoms to isotropic. 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 9 8.98 5 P 6 5.49 5 S 62 5.16 5 C 7105 2.51 5 N 1818 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10996 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: 5001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5001 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 26, 'TRANS': 646} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.58, per 1000 atoms: 0.60 Number of scatterers: 10996 At special positions: 0 Unit cell: (89.056, 112.332, 143.704, 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 9 19.00 S 62 16.00 P 6 15.00 O 1996 8.00 N 1818 7.00 C 7105 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 - 3.50 Amino acid : False - 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: 4.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 63.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.788A 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 178 through 192 Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.361A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.558A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 304 removed outlier: 4.566A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.401A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.787A 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 Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.365A 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 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.028A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 550 removed outlier: 4.209A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 34 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 133 through 149 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.550A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 23 removed outlier: 4.272A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 63 through 103 removed outlier: 3.751A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 246 removed outlier: 4.048A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.761A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.986A 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 265 through 284 removed outlier: 5.522A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.939A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 556 through 582 removed outlier: 3.995A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 5.010A 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 606 removed outlier: 3.654A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.458A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.327A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix 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 removed outlier: 3.572A pdb=" N LYS A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.409A 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 119 through 120 removed outlier: 3.720A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.522A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 288 removed outlier: 6.411A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP B 518 " --> pdb=" O PHD B 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.957A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET B 383 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 377 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1771 1.31 - 1.44: 2725 1.44 - 1.57: 6563 1.57 - 1.69: 13 1.69 - 1.82: 112 Bond restraints: 11184 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.592 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.424 -0.090 1.10e-02 8.26e+03 6.76e+01 bond pdb=" CB7 CDL A 608 " pdb=" OB8 CDL A 608 " ideal model delta sigma weight residual 1.334 1.422 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CA7 CDL A 608 " pdb=" OA8 CDL A 608 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.43e+01 bond pdb=" CA7 CDL A 609 " pdb=" OA8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.414 -0.080 1.10e-02 8.26e+03 5.28e+01 ... (remaining 11179 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.81: 232 104.81 - 112.16: 5776 112.16 - 119.51: 3739 119.51 - 126.86: 5290 126.86 - 134.21: 140 Bond angle restraints: 15177 Sorted by residual: angle pdb=" C51 CDL A 609 " pdb=" CB5 CDL A 609 " pdb=" OB6 CDL A 609 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL A 608 " pdb=" CA5 CDL A 608 " pdb=" OA6 CDL A 608 " ideal model delta sigma weight residual 111.33 120.12 -8.79 1.32e+00 5.72e-01 4.42e+01 angle pdb=" C11 CDL A 609 " pdb=" CA5 CDL A 609 " pdb=" OA6 CDL A 609 " ideal model delta sigma weight residual 111.33 119.83 -8.50 1.32e+00 5.72e-01 4.14e+01 angle pdb=" C51 CDL A 608 " pdb=" CB5 CDL A 608 " pdb=" OB6 CDL A 608 " ideal model delta sigma weight residual 111.33 119.63 -8.30 1.32e+00 5.72e-01 3.94e+01 angle pdb=" C71 CDL A 609 " pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 111.64 120.47 -8.83 1.65e+00 3.69e-01 2.88e+01 ... (remaining 15172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5890 17.92 - 35.85: 624 35.85 - 53.77: 152 53.77 - 71.70: 44 71.70 - 89.62: 12 Dihedral angle restraints: 6722 sinusoidal: 2625 harmonic: 4097 Sorted by residual: dihedral pdb=" C PHD B 307 " pdb=" N PHD B 307 " pdb=" CA PHD B 307 " pdb=" CB PHD B 307 " ideal model delta harmonic sigma weight residual -122.60 -137.22 14.62 0 2.50e+00 1.60e-01 3.42e+01 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 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" N PHD B 307 " pdb=" C PHD B 307 " pdb=" CA PHD B 307 " pdb=" CB PHD B 307 " ideal model delta harmonic sigma weight residual 122.80 134.98 -12.18 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 6719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1729 0.104 - 0.207: 73 0.207 - 0.311: 4 0.311 - 0.414: 0 0.414 - 0.518: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA PHD B 307 " pdb=" N PHD B 307 " pdb=" C PHD B 307 " pdb=" CB PHD B 307 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA LEU B 342 " pdb=" N LEU B 342 " pdb=" C LEU B 342 " pdb=" CB LEU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE B 393 " pdb=" CA ILE B 393 " pdb=" CG1 ILE B 393 " pdb=" CG2 ILE B 393 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1804 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A 362 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 360 " 0.011 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE B 360 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 360 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 360 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 360 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 360 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 360 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 18 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C THR C 18 " -0.037 2.00e-02 2.50e+03 pdb=" O THR C 18 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 2986 2.81 - 3.39: 12509 3.39 - 3.98: 21778 3.98 - 4.56: 30403 4.56 - 5.14: 44182 Nonbonded interactions: 111858 Sorted by model distance: nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 339 " pdb=" O CYS A 344 " model vdw 2.248 2.440 nonbonded pdb=" O TYR C 22 " pdb=" OG1 THR C 26 " model vdw 2.270 2.440 nonbonded pdb=" OG SER B 612 " pdb=" OD1 ASP B 614 " model vdw 2.271 2.440 nonbonded pdb=" OG SER A 241 " pdb=" O ILE A 348 " model vdw 2.278 2.440 ... (remaining 111853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.300 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 11184 Z= 0.439 Angle : 0.929 11.183 15177 Z= 0.471 Chirality : 0.049 0.518 1807 Planarity : 0.006 0.080 1905 Dihedral : 16.337 89.620 4090 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1433 helix: 0.17 (0.16), residues: 884 sheet: -1.05 (0.58), residues: 82 loop : -1.79 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS B 563 PHE 0.037 0.002 PHE B 360 TYR 0.030 0.002 TYR B 114 ARG 0.007 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8414 (mt) cc_final: 0.8142 (mt) REVERT: A 365 LEU cc_start: 0.7752 (tp) cc_final: 0.7523 (tp) REVERT: B 186 TRP cc_start: 0.6306 (p-90) cc_final: 0.5586 (p-90) REVERT: B 279 MET cc_start: 0.7084 (mmm) cc_final: 0.6817 (mtm) REVERT: B 393 ILE cc_start: 0.6839 (mm) cc_final: 0.6596 (mm) REVERT: B 515 MET cc_start: 0.6470 (tmm) cc_final: 0.5536 (tmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2120 time to fit residues: 48.9918 Evaluate side-chains 134 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 39 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11184 Z= 0.171 Angle : 0.538 7.311 15177 Z= 0.271 Chirality : 0.040 0.160 1807 Planarity : 0.004 0.064 1905 Dihedral : 11.149 67.684 1714 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.80 % Allowed : 7.69 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1433 helix: 1.18 (0.17), residues: 872 sheet: -0.98 (0.55), residues: 92 loop : -1.64 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 655 HIS 0.002 0.000 HIS A 451 PHE 0.011 0.001 PHE A 490 TYR 0.029 0.001 TYR A 381 ARG 0.002 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.138 Fit side-chains REVERT: A 27 LEU cc_start: 0.8442 (mt) cc_final: 0.8188 (mt) REVERT: A 365 LEU cc_start: 0.7867 (tp) cc_final: 0.7624 (tp) REVERT: B 186 TRP cc_start: 0.6294 (p-90) cc_final: 0.5328 (p-90) REVERT: B 279 MET cc_start: 0.7285 (mmm) cc_final: 0.6978 (mmt) REVERT: B 469 MET cc_start: 0.7835 (ppp) cc_final: 0.7498 (ptt) REVERT: B 515 MET cc_start: 0.6386 (tmm) cc_final: 0.6055 (tmm) outliers start: 9 outliers final: 5 residues processed: 147 average time/residue: 0.1906 time to fit residues: 42.3039 Evaluate side-chains 138 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 0.0000 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11184 Z= 0.394 Angle : 0.680 10.998 15177 Z= 0.343 Chirality : 0.045 0.172 1807 Planarity : 0.005 0.063 1905 Dihedral : 10.768 60.538 1714 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.94 % Allowed : 12.01 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1433 helix: 0.87 (0.17), residues: 884 sheet: -1.23 (0.54), residues: 93 loop : -1.62 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 655 HIS 0.004 0.001 HIS A 451 PHE 0.020 0.002 PHE A 471 TYR 0.034 0.003 TYR A 381 ARG 0.004 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.231 Fit side-chains REVERT: A 27 LEU cc_start: 0.8539 (mt) cc_final: 0.8272 (mt) REVERT: B 87 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6969 (mt-10) REVERT: B 186 TRP cc_start: 0.6283 (p-90) cc_final: 0.5907 (p-90) REVERT: B 279 MET cc_start: 0.7231 (mmm) cc_final: 0.6945 (mmt) REVERT: B 469 MET cc_start: 0.7854 (ppp) cc_final: 0.7305 (ptt) REVERT: B 515 MET cc_start: 0.6679 (tmm) cc_final: 0.6191 (tmm) outliers start: 22 outliers final: 16 residues processed: 148 average time/residue: 0.2020 time to fit residues: 45.3310 Evaluate side-chains 144 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 93 GLN B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11184 Z= 0.181 Angle : 0.545 9.837 15177 Z= 0.273 Chirality : 0.040 0.163 1807 Planarity : 0.004 0.049 1905 Dihedral : 10.170 59.984 1714 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.24 % Allowed : 14.40 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1433 helix: 1.34 (0.17), residues: 870 sheet: -1.29 (0.53), residues: 93 loop : -1.51 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.002 0.001 HIS B 404 PHE 0.011 0.001 PHE A 260 TYR 0.026 0.002 TYR A 381 ARG 0.004 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.178 Fit side-chains REVERT: A 27 LEU cc_start: 0.8512 (mt) cc_final: 0.8225 (mt) REVERT: B 186 TRP cc_start: 0.6363 (p-90) cc_final: 0.5977 (p-90) REVERT: B 279 MET cc_start: 0.7283 (mmm) cc_final: 0.6948 (mmt) REVERT: B 393 ILE cc_start: 0.6616 (mm) cc_final: 0.6384 (mm) REVERT: B 469 MET cc_start: 0.7578 (ppp) cc_final: 0.7272 (ptt) REVERT: B 515 MET cc_start: 0.6638 (tmm) cc_final: 0.6259 (tmm) outliers start: 14 outliers final: 6 residues processed: 143 average time/residue: 0.2142 time to fit residues: 46.1179 Evaluate side-chains 133 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11184 Z= 0.208 Angle : 0.550 9.247 15177 Z= 0.275 Chirality : 0.040 0.162 1807 Planarity : 0.004 0.045 1905 Dihedral : 9.911 59.928 1714 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.77 % Allowed : 15.37 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1433 helix: 1.45 (0.17), residues: 872 sheet: -1.33 (0.54), residues: 93 loop : -1.43 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE B 360 TYR 0.025 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.108 Fit side-chains REVERT: A 27 LEU cc_start: 0.8502 (mt) cc_final: 0.8220 (mt) REVERT: C 1 MET cc_start: 0.5306 (mtm) cc_final: 0.4783 (mtt) REVERT: C 128 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B 87 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6985 (mt-10) REVERT: B 133 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6645 (pp) REVERT: B 186 TRP cc_start: 0.6397 (p-90) cc_final: 0.5449 (p-90) REVERT: B 279 MET cc_start: 0.7191 (mmm) cc_final: 0.6891 (mmt) REVERT: B 393 ILE cc_start: 0.6578 (mm) cc_final: 0.6364 (mm) REVERT: B 469 MET cc_start: 0.7547 (ppp) cc_final: 0.7317 (ptt) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.1985 time to fit residues: 43.4124 Evaluate side-chains 140 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11184 Z= 0.224 Angle : 0.556 9.415 15177 Z= 0.278 Chirality : 0.041 0.162 1807 Planarity : 0.004 0.043 1905 Dihedral : 9.773 59.430 1714 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.86 % Allowed : 15.55 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1433 helix: 1.45 (0.17), residues: 872 sheet: -1.35 (0.52), residues: 99 loop : -1.40 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 32 HIS 0.002 0.001 HIS B 404 PHE 0.013 0.001 PHE B 360 TYR 0.025 0.002 TYR A 381 ARG 0.002 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.213 Fit side-chains REVERT: A 27 LEU cc_start: 0.8496 (mt) cc_final: 0.8216 (mt) REVERT: A 363 MET cc_start: 0.8457 (ttm) cc_final: 0.8209 (ttm) REVERT: C 1 MET cc_start: 0.5423 (mtm) cc_final: 0.4910 (mtt) REVERT: C 128 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 51 ILE cc_start: 0.7898 (mm) cc_final: 0.7541 (mm) REVERT: B 133 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6949 (pp) REVERT: B 186 TRP cc_start: 0.6267 (p-90) cc_final: 0.5272 (p-90) REVERT: B 187 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6933 (tp) REVERT: B 279 MET cc_start: 0.7228 (mmm) cc_final: 0.6900 (mmt) REVERT: B 515 MET cc_start: 0.6772 (tmm) cc_final: 0.6321 (tmm) outliers start: 21 outliers final: 14 residues processed: 150 average time/residue: 0.1990 time to fit residues: 45.0398 Evaluate side-chains 146 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11184 Z= 0.170 Angle : 0.535 9.251 15177 Z= 0.266 Chirality : 0.040 0.165 1807 Planarity : 0.004 0.040 1905 Dihedral : 9.445 59.816 1714 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.77 % Allowed : 16.34 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1433 helix: 1.58 (0.17), residues: 871 sheet: -1.36 (0.51), residues: 99 loop : -1.36 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.001 0.000 HIS B 404 PHE 0.017 0.001 PHE B 360 TYR 0.024 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.328 Fit side-chains REVERT: A 27 LEU cc_start: 0.8480 (mt) cc_final: 0.8190 (mt) REVERT: A 363 MET cc_start: 0.8423 (ttm) cc_final: 0.8198 (ttm) REVERT: C 1 MET cc_start: 0.5341 (mtm) cc_final: 0.4781 (mtt) REVERT: C 128 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8278 (mt) REVERT: B 51 ILE cc_start: 0.7933 (mm) cc_final: 0.7590 (mm) REVERT: B 87 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6959 (mt-10) REVERT: B 133 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6963 (pp) REVERT: B 186 TRP cc_start: 0.6318 (p-90) cc_final: 0.5323 (p-90) REVERT: B 187 LEU cc_start: 0.7166 (tp) cc_final: 0.6925 (tp) REVERT: B 279 MET cc_start: 0.7175 (mmm) cc_final: 0.6874 (mmt) REVERT: B 471 THR cc_start: 0.7248 (m) cc_final: 0.7045 (p) REVERT: B 515 MET cc_start: 0.6786 (tmm) cc_final: 0.6367 (tmm) REVERT: B 629 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8279 (t) outliers start: 20 outliers final: 12 residues processed: 157 average time/residue: 0.2054 time to fit residues: 48.4689 Evaluate side-chains 148 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11184 Z= 0.231 Angle : 0.575 10.315 15177 Z= 0.284 Chirality : 0.041 0.163 1807 Planarity : 0.004 0.041 1905 Dihedral : 9.467 59.472 1714 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.86 % Allowed : 16.96 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1433 helix: 1.47 (0.17), residues: 880 sheet: -1.37 (0.51), residues: 99 loop : -1.38 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.002 0.001 HIS A 451 PHE 0.017 0.001 PHE B 360 TYR 0.026 0.002 TYR A 381 ARG 0.002 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.204 Fit side-chains REVERT: A 27 LEU cc_start: 0.8497 (mt) cc_final: 0.8215 (mt) REVERT: A 363 MET cc_start: 0.8475 (ttm) cc_final: 0.8243 (ttm) REVERT: C 128 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 51 ILE cc_start: 0.7910 (mm) cc_final: 0.7539 (mm) REVERT: B 87 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6961 (mm-30) REVERT: B 133 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6973 (pp) REVERT: B 186 TRP cc_start: 0.6441 (p-90) cc_final: 0.5440 (p-90) REVERT: B 187 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6941 (tp) REVERT: B 279 MET cc_start: 0.7252 (mmm) cc_final: 0.6925 (mmt) REVERT: B 471 THR cc_start: 0.7348 (m) cc_final: 0.7138 (p) REVERT: B 515 MET cc_start: 0.6788 (tmm) cc_final: 0.6383 (tmm) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 0.1965 time to fit residues: 43.9335 Evaluate side-chains 151 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11184 Z= 0.179 Angle : 0.557 11.863 15177 Z= 0.274 Chirality : 0.040 0.166 1807 Planarity : 0.004 0.040 1905 Dihedral : 9.265 59.767 1714 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.77 % Allowed : 17.40 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1433 helix: 1.58 (0.18), residues: 871 sheet: -1.34 (0.51), residues: 99 loop : -1.33 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 139 HIS 0.001 0.000 HIS B 404 PHE 0.019 0.001 PHE B 360 TYR 0.024 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.211 Fit side-chains REVERT: A 27 LEU cc_start: 0.8478 (mt) cc_final: 0.8185 (mt) REVERT: A 363 MET cc_start: 0.8441 (ttm) cc_final: 0.8232 (ttm) REVERT: C 128 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8278 (mt) REVERT: B 51 ILE cc_start: 0.7930 (mm) cc_final: 0.7585 (mm) REVERT: B 87 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 133 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6979 (pp) REVERT: B 186 TRP cc_start: 0.6418 (p-90) cc_final: 0.5434 (p-90) REVERT: B 187 LEU cc_start: 0.7182 (tp) cc_final: 0.6936 (tp) REVERT: B 515 MET cc_start: 0.6754 (tmm) cc_final: 0.6351 (tmm) REVERT: B 629 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8268 (t) outliers start: 20 outliers final: 15 residues processed: 154 average time/residue: 0.2118 time to fit residues: 49.8703 Evaluate side-chains 149 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 0.0060 chunk 90 optimal weight: 9.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11184 Z= 0.199 Angle : 0.575 14.609 15177 Z= 0.280 Chirality : 0.041 0.205 1807 Planarity : 0.004 0.041 1905 Dihedral : 9.223 59.818 1714 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.86 % Allowed : 17.49 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1433 helix: 1.53 (0.17), residues: 873 sheet: -1.34 (0.51), residues: 99 loop : -1.29 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 33 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE B 578 TYR 0.025 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.184 Fit side-chains REVERT: A 27 LEU cc_start: 0.8474 (mt) cc_final: 0.8193 (mt) REVERT: A 363 MET cc_start: 0.8450 (ttm) cc_final: 0.8229 (ttm) REVERT: C 128 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8262 (mt) REVERT: B 51 ILE cc_start: 0.7907 (mm) cc_final: 0.7560 (mm) REVERT: B 87 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6944 (mm-30) REVERT: B 133 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6936 (pp) REVERT: B 186 TRP cc_start: 0.6349 (p-90) cc_final: 0.5391 (p-90) REVERT: B 187 LEU cc_start: 0.7196 (tp) cc_final: 0.6947 (tp) REVERT: B 279 MET cc_start: 0.7323 (mmm) cc_final: 0.7005 (mmm) REVERT: B 515 MET cc_start: 0.6753 (tmm) cc_final: 0.6353 (tmm) REVERT: B 629 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8279 (t) outliers start: 21 outliers final: 16 residues processed: 148 average time/residue: 0.1915 time to fit residues: 43.2752 Evaluate side-chains 148 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103560 restraints weight = 14485.249| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.35 r_work: 0.3057 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11184 Z= 0.166 Angle : 0.554 12.798 15177 Z= 0.271 Chirality : 0.040 0.174 1807 Planarity : 0.004 0.040 1905 Dihedral : 9.048 59.836 1714 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.68 % Allowed : 17.93 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1433 helix: 1.63 (0.18), residues: 871 sheet: -1.19 (0.56), residues: 82 loop : -1.29 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 33 HIS 0.001 0.000 HIS B 404 PHE 0.010 0.001 PHE B 578 TYR 0.024 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.63 seconds wall clock time: 40 minutes 38.50 seconds (2438.50 seconds total)