Starting phenix.real_space_refine on Fri Mar 15 08:37:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/03_2024/7zre_14912_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/03_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_14912/03_2024/7zre_14912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/03_2024/7zre_14912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/03_2024/7zre_14912_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zre_14912/03_2024/7zre_14912_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.00, per 1000 atoms: 0.55 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: 4.39 Conformation dependent library (CDL) restraints added in 2.1 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... running ksdssp... Secondary structure from input PDB file: 54 helices and 5 sheets defined 56.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 134 through 156 removed outlier: 3.788A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 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 277 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 356 through 367 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 378 through 398 Processing helix chain 'A' and resid 411 through 436 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 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.513A pdb=" N LEU A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 2 through 33 Proline residue: C 6 - end of helix Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 148 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.272A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 64 through 102 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) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 245 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) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 266 through 285 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 292 through 300 Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.528A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 367 through 370 No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 509 removed outlier: 4.481A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 557 through 594 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) removed outlier: 4.359A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.654A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 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 632 through 637 Processing helix chain 'B' and resid 646 through 679 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= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.522A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 531 through 535 removed outlier: 6.577A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ASP B 518 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 373 through 375 removed outlier: 4.346A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 317 through 323 removed outlier: 7.646A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1653 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: 3.08 Time building geometry restraints manager: 4.73 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: 2998 2.81 - 3.39: 12628 3.39 - 3.98: 22007 3.98 - 4.56: 30532 4.56 - 5.14: 44185 Nonbonded interactions: 112350 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 112345 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.840 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- 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= 0.400 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 : 1.316 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: 0.2206 time to fit residues: 51.5737 Evaluate side-chains 134 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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: 6.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.0040 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11184 Z= 0.160 Angle : 0.520 7.339 15177 Z= 0.262 Chirality : 0.039 0.149 1807 Planarity : 0.004 0.064 1905 Dihedral : 11.148 67.796 1714 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.80 % Allowed : 7.51 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.21), residues: 1433 helix: 1.01 (0.17), residues: 881 sheet: -0.97 (0.58), residues: 80 loop : -1.72 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 655 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE A 490 TYR 0.026 0.002 TYR A 381 ARG 0.002 0.000 ARG B 504 *********************** 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 150 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.121 Fit side-chains REVERT: A 27 LEU cc_start: 0.8401 (mt) cc_final: 0.8150 (mt) REVERT: A 365 LEU cc_start: 0.7864 (tp) cc_final: 0.7660 (tp) REVERT: B 186 TRP cc_start: 0.6299 (p-90) cc_final: 0.5365 (p-90) REVERT: B 279 MET cc_start: 0.7282 (mmm) cc_final: 0.6984 (mmt) REVERT: B 342 LEU cc_start: 0.8689 (tp) cc_final: 0.8488 (tp) REVERT: B 393 ILE cc_start: 0.6821 (mm) cc_final: 0.6488 (mm) REVERT: B 469 MET cc_start: 0.7938 (ppp) cc_final: 0.7102 (ppp) REVERT: B 515 MET cc_start: 0.6247 (tmm) cc_final: 0.5878 (tmm) outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.1925 time to fit residues: 42.1390 Evaluate side-chains 134 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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: 0.0060 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 0.0670 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.6140 ------------------------------------------------------------------------------- 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** C 37 GLN B 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11184 Z= 0.338 Angle : 0.629 9.943 15177 Z= 0.317 Chirality : 0.043 0.167 1807 Planarity : 0.005 0.059 1905 Dihedral : 10.608 59.519 1714 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.59 % Allowed : 11.31 % Favored : 87.10 % 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: -0.08 (0.21), residues: 1433 helix: 0.87 (0.17), residues: 880 sheet: -1.28 (0.51), residues: 97 loop : -1.52 (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 0.019 0.002 PHE A 471 TYR 0.033 0.003 TYR A 381 ARG 0.006 0.000 ARG A 326 *********************** 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 158 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.135 Fit side-chains REVERT: A 27 LEU cc_start: 0.8497 (mt) cc_final: 0.8232 (mt) REVERT: B 87 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6985 (mt-10) REVERT: B 186 TRP cc_start: 0.6312 (p-90) cc_final: 0.5966 (p-90) REVERT: B 279 MET cc_start: 0.7300 (mmm) cc_final: 0.6999 (mmt) REVERT: B 469 MET cc_start: 0.7954 (ppp) cc_final: 0.7300 (ppp) REVERT: B 515 MET cc_start: 0.6405 (tmm) cc_final: 0.6005 (tmm) outliers start: 18 outliers final: 11 residues processed: 151 average time/residue: 0.1963 time to fit residues: 44.8948 Evaluate side-chains 143 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain C residue 10 THR 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 283 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 ILE 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: 0.7980 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11184 Z= 0.156 Angle : 0.521 8.209 15177 Z= 0.261 Chirality : 0.039 0.180 1807 Planarity : 0.004 0.047 1905 Dihedral : 10.009 59.732 1714 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.15 % Allowed : 14.05 % Favored : 84.81 % 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: 0.32 (0.22), residues: 1433 helix: 1.22 (0.17), residues: 877 sheet: -1.22 (0.52), residues: 93 loop : -1.41 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.001 0.000 HIS A 451 PHE 0.010 0.001 PHE B 578 TYR 0.026 0.002 TYR A 381 ARG 0.002 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 156 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.100 Fit side-chains REVERT: A 27 LEU cc_start: 0.8489 (mt) cc_final: 0.8221 (mt) REVERT: B 87 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6950 (mt-10) REVERT: B 186 TRP cc_start: 0.6371 (p-90) cc_final: 0.5939 (p-90) REVERT: B 279 MET cc_start: 0.7359 (mmm) cc_final: 0.7041 (mmt) REVERT: B 383 MET cc_start: 0.5903 (tpp) cc_final: 0.5648 (tpp) REVERT: B 469 MET cc_start: 0.7834 (ppp) cc_final: 0.6960 (ppp) REVERT: B 515 MET cc_start: 0.6414 (tmm) cc_final: 0.6099 (tmm) outliers start: 13 outliers final: 7 residues processed: 151 average time/residue: 0.1998 time to fit residues: 45.3773 Evaluate side-chains 141 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE 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 558 LEU 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: 8.9990 chunk 78 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 279 GLN ** 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: 0.7690 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11184 Z= 0.181 Angle : 0.520 7.869 15177 Z= 0.260 Chirality : 0.040 0.152 1807 Planarity : 0.004 0.043 1905 Dihedral : 9.705 59.248 1714 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.86 % Allowed : 14.49 % Favored : 83.66 % 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: 0.44 (0.22), residues: 1433 helix: 1.34 (0.18), residues: 873 sheet: -1.26 (0.50), residues: 99 loop : -1.38 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 655 HIS 0.002 0.001 HIS A 451 PHE 0.010 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 156 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.411 Fit side-chains REVERT: A 27 LEU cc_start: 0.8495 (mt) cc_final: 0.8215 (mt) REVERT: A 445 MET cc_start: 0.7830 (mmt) cc_final: 0.7358 (mmt) REVERT: C 128 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 87 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6946 (mt-10) REVERT: B 186 TRP cc_start: 0.6386 (p-90) cc_final: 0.5418 (p-90) REVERT: B 279 MET cc_start: 0.7227 (mmm) cc_final: 0.6930 (mmt) REVERT: B 383 MET cc_start: 0.6025 (tpp) cc_final: 0.5820 (tpp) REVERT: B 469 MET cc_start: 0.7810 (ppp) cc_final: 0.6804 (ppp) REVERT: B 629 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8152 (t) outliers start: 21 outliers final: 10 residues processed: 154 average time/residue: 0.2167 time to fit residues: 50.1955 Evaluate side-chains 142 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 387 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 311 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 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: 2.9990 chunk 124 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11184 Z= 0.200 Angle : 0.531 8.142 15177 Z= 0.265 Chirality : 0.040 0.150 1807 Planarity : 0.004 0.040 1905 Dihedral : 9.592 59.213 1714 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.21 % Allowed : 14.75 % Favored : 83.04 % 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: 0.45 (0.22), residues: 1433 helix: 1.31 (0.18), residues: 878 sheet: -1.17 (0.57), residues: 77 loop : -1.32 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 139 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE B 360 TYR 0.023 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** 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 160 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.186 Fit side-chains REVERT: A 27 LEU cc_start: 0.8498 (mt) cc_final: 0.8218 (mt) REVERT: A 320 MET cc_start: 0.8885 (mmm) cc_final: 0.8508 (mmt) REVERT: A 445 MET cc_start: 0.8031 (mmt) cc_final: 0.7590 (mmt) REVERT: C 128 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8249 (mt) REVERT: C 141 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8473 (mp) REVERT: B 51 ILE cc_start: 0.7906 (mm) cc_final: 0.7552 (mm) REVERT: B 186 TRP cc_start: 0.6427 (p-90) cc_final: 0.5471 (p-90) REVERT: B 279 MET cc_start: 0.7196 (mmm) cc_final: 0.6878 (mmt) REVERT: B 515 MET cc_start: 0.6681 (tmm) cc_final: 0.6220 (tmm) REVERT: B 629 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8115 (t) outliers start: 25 outliers final: 19 residues processed: 155 average time/residue: 0.2029 time to fit residues: 47.3462 Evaluate side-chains 152 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 THR 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 C residue 10 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 442 VAL 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: 0.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 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: 0.7649 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11184 Z= 0.133 Angle : 0.509 9.689 15177 Z= 0.250 Chirality : 0.038 0.143 1807 Planarity : 0.003 0.039 1905 Dihedral : 9.196 59.883 1714 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.50 % Allowed : 15.72 % Favored : 82.77 % 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: 0.70 (0.22), residues: 1433 helix: 1.54 (0.18), residues: 868 sheet: -1.19 (0.57), residues: 79 loop : -1.21 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.001 0.000 HIS B 404 PHE 0.014 0.001 PHE B 360 TYR 0.022 0.001 TYR A 381 ARG 0.002 0.000 ARG C 5 *********************** 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 154 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.236 Fit side-chains REVERT: A 27 LEU cc_start: 0.8439 (mt) cc_final: 0.8136 (mt) REVERT: A 320 MET cc_start: 0.8892 (mmm) cc_final: 0.8532 (mmt) REVERT: A 445 MET cc_start: 0.7951 (mmt) cc_final: 0.7584 (mmt) REVERT: C 141 ILE cc_start: 0.8773 (mt) cc_final: 0.8529 (mp) REVERT: B 51 ILE cc_start: 0.7938 (mm) cc_final: 0.7608 (mm) REVERT: B 87 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6972 (mt-10) REVERT: B 186 TRP cc_start: 0.6404 (p-90) cc_final: 0.5449 (p-90) REVERT: B 383 MET cc_start: 0.5101 (tpp) cc_final: 0.4872 (tpp) REVERT: B 469 MET cc_start: 0.7602 (ppp) cc_final: 0.6815 (ptt) REVERT: B 515 MET cc_start: 0.6723 (tmm) cc_final: 0.6248 (tmm) REVERT: B 629 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8070 (t) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.1938 time to fit residues: 44.0494 Evaluate side-chains 146 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain D residue 14 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 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: 0.7980 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1934 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= 0.220 Angle : 0.558 14.387 15177 Z= 0.272 Chirality : 0.041 0.159 1807 Planarity : 0.004 0.041 1905 Dihedral : 9.307 59.957 1714 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.12 % Allowed : 15.37 % Favored : 82.51 % 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: 0.58 (0.22), residues: 1433 helix: 1.38 (0.18), residues: 879 sheet: -1.09 (0.58), residues: 77 loop : -1.22 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.002 0.001 HIS A 451 PHE 0.015 0.001 PHE B 360 TYR 0.028 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 159 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.202 Fit side-chains REVERT: A 27 LEU cc_start: 0.8493 (mt) cc_final: 0.8208 (mt) REVERT: A 445 MET cc_start: 0.8166 (mmt) cc_final: 0.7711 (mmt) REVERT: C 141 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 51 ILE cc_start: 0.7927 (mm) cc_final: 0.7553 (mm) REVERT: B 87 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6992 (mt-10) REVERT: B 133 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6596 (pp) REVERT: B 186 TRP cc_start: 0.6338 (p-90) cc_final: 0.5433 (p-90) REVERT: B 279 MET cc_start: 0.7307 (mmm) cc_final: 0.7019 (mmm) REVERT: B 469 MET cc_start: 0.7624 (ppp) cc_final: 0.6863 (ptt) REVERT: B 515 MET cc_start: 0.6668 (tmm) cc_final: 0.6189 (tmm) REVERT: B 629 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8074 (t) outliers start: 24 outliers final: 18 residues processed: 154 average time/residue: 0.1961 time to fit residues: 45.7265 Evaluate side-chains 152 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 130 MET 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 60 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 141 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11184 Z= 0.140 Angle : 0.529 11.783 15177 Z= 0.256 Chirality : 0.039 0.147 1807 Planarity : 0.003 0.039 1905 Dihedral : 9.073 59.093 1714 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.50 % Allowed : 16.34 % Favored : 82.16 % 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: 0.72 (0.22), residues: 1433 helix: 1.54 (0.18), residues: 869 sheet: -1.17 (0.57), residues: 79 loop : -1.19 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 32 HIS 0.001 0.000 HIS A 451 PHE 0.010 0.001 PHE B 578 TYR 0.023 0.001 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 149 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.223 Fit side-chains REVERT: A 27 LEU cc_start: 0.8429 (mt) cc_final: 0.8134 (mt) REVERT: A 445 MET cc_start: 0.8092 (mmt) cc_final: 0.7716 (mmt) REVERT: C 141 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 51 ILE cc_start: 0.7915 (mm) cc_final: 0.7576 (mm) REVERT: B 87 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6941 (mt-10) REVERT: B 186 TRP cc_start: 0.6425 (p-90) cc_final: 0.5445 (p-90) REVERT: B 279 MET cc_start: 0.7297 (mmm) cc_final: 0.7002 (mmm) REVERT: B 393 ILE cc_start: 0.6617 (mm) cc_final: 0.6327 (mm) REVERT: B 469 MET cc_start: 0.7607 (ppp) cc_final: 0.6801 (ptt) REVERT: B 515 MET cc_start: 0.6674 (tmm) cc_final: 0.6195 (tmm) REVERT: B 629 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8036 (t) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.1989 time to fit residues: 43.2690 Evaluate side-chains 144 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 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: 0.0980 chunk 82 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 113 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11184 Z= 0.156 Angle : 0.531 11.375 15177 Z= 0.258 Chirality : 0.039 0.150 1807 Planarity : 0.003 0.040 1905 Dihedral : 9.010 59.902 1714 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.50 % Allowed : 16.34 % Favored : 82.16 % 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: 0.75 (0.22), residues: 1433 helix: 1.56 (0.18), residues: 868 sheet: -1.17 (0.57), residues: 79 loop : -1.16 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 33 HIS 0.001 0.000 HIS A 85 PHE 0.010 0.001 PHE B 578 TYR 0.024 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 145 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.238 Fit side-chains REVERT: A 27 LEU cc_start: 0.8429 (mt) cc_final: 0.8136 (mt) REVERT: A 445 MET cc_start: 0.8144 (mmt) cc_final: 0.7841 (mmt) REVERT: C 141 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8555 (mp) REVERT: B 51 ILE cc_start: 0.7921 (mm) cc_final: 0.7576 (mm) REVERT: B 87 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6944 (mt-10) REVERT: B 133 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6623 (pp) REVERT: B 186 TRP cc_start: 0.6354 (p-90) cc_final: 0.5465 (p-90) REVERT: B 279 MET cc_start: 0.7280 (mmm) cc_final: 0.6969 (mmm) REVERT: B 393 ILE cc_start: 0.6638 (mm) cc_final: 0.6346 (mm) REVERT: B 469 MET cc_start: 0.7595 (ppp) cc_final: 0.6824 (ptt) REVERT: B 515 MET cc_start: 0.6679 (tmm) cc_final: 0.6199 (tmm) REVERT: B 629 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8047 (t) outliers start: 17 outliers final: 13 residues processed: 140 average time/residue: 0.2030 time to fit residues: 43.2946 Evaluate side-chains 145 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 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 120 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.0570 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 112 ASN C 39 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109098 restraints weight = 14229.639| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.31 r_work: 0.3104 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11184 Z= 0.136 Angle : 0.518 11.157 15177 Z= 0.251 Chirality : 0.039 0.147 1807 Planarity : 0.003 0.039 1905 Dihedral : 8.822 59.924 1714 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.50 % Allowed : 16.61 % 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: 0.82 (0.22), residues: 1433 helix: 1.63 (0.18), residues: 863 sheet: -1.18 (0.57), residues: 79 loop : -1.13 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 33 HIS 0.001 0.000 HIS A 451 PHE 0.010 0.001 PHE B 578 TYR 0.023 0.001 TYR A 381 ARG 0.001 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.11 seconds wall clock time: 42 minutes 6.81 seconds (2526.81 seconds total)