Starting phenix.real_space_refine on Wed Sep 17 15:51:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zue_60482/09_2025/8zue_60482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zue_60482/09_2025/8zue_60482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zue_60482/09_2025/8zue_60482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zue_60482/09_2025/8zue_60482.map" model { file = "/net/cci-nas-00/data/ceres_data/8zue_60482/09_2025/8zue_60482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zue_60482/09_2025/8zue_60482.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6064 2.51 5 N 1652 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4313 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 18, 'TRANS': 512} Chain: "B" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5223 Classifications: {'peptide': 651} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 629} Chain breaks: 3 Time building chain proxies: 2.17, per 1000 atoms: 0.23 Number of scatterers: 9536 At special positions: 0 Unit cell: (82.39, 115.56, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1788 8.00 N 1652 7.00 C 6064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 280.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 53.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.583A pdb=" N ILE A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.965A pdb=" N THR A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 123' Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 170 through 191 removed outlier: 3.667A pdb=" N LEU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.720A pdb=" N ALA A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.935A pdb=" N ASP A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 Processing helix chain 'A' and resid 336 through 357 removed outlier: 4.307A pdb=" N GLU A 342 " --> pdb=" O HIS A 338 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Proline residue: A 410 - end of helix Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.416A pdb=" N ILE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.795A pdb=" N ASP A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 485 through 497 removed outlier: 3.684A pdb=" N LYS A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.636A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 18 through 32 removed outlier: 3.727A pdb=" N ASN B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 56 through 68 removed outlier: 3.730A pdb=" N LEU B 60 " --> pdb=" O HIS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.819A pdb=" N PHE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.563A pdb=" N ARG B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 290 through 305 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 424 through 433 Processing helix chain 'B' and resid 513 through 522 removed outlier: 4.108A pdb=" N SER B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 539 through 552 removed outlier: 3.798A pdb=" N THR B 543 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 removed outlier: 3.504A pdb=" N PHE B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 Processing helix chain 'B' and resid 581 through 599 removed outlier: 4.021A pdb=" N GLN B 595 " --> pdb=" O ASP B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 618 removed outlier: 3.688A pdb=" N ASN B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 643 removed outlier: 3.885A pdb=" N GLU B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 668 through 673 removed outlier: 4.005A pdb=" N ILE B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 3.518A pdb=" N ARG B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 704 Processing helix chain 'B' and resid 704 through 711 removed outlier: 3.668A pdb=" N TRP B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 710 " --> pdb=" O ASP B 706 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 7.544A pdb=" N GLU A 166 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 108 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 39 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 8.649A pdb=" N HIS A 514 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE A 464 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A 392 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 465 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A 394 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 379 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU A 378 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 366 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 400 removed outlier: 4.190A pdb=" N ASP A 471 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR A 470 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.873A pdb=" N PHE B 205 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR B 250 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE B 207 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 204 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B 208 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 144 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 146 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 278 through 283 removed outlier: 7.071A pdb=" N ALA B 402 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 437 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASN B 404 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS B 439 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B 406 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE B 441 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 309 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS B 390 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE B 311 " --> pdb=" O CYS B 390 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3169 1.34 - 1.46: 2031 1.46 - 1.58: 4479 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 9728 Sorted by residual: bond pdb=" CA PHE A 483 " pdb=" CB PHE A 483 " ideal model delta sigma weight residual 1.527 1.548 -0.021 1.15e-02 7.56e+03 3.35e+00 bond pdb=" CA ASP A 437 " pdb=" CB ASP A 437 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.24e+00 bond pdb=" CB GLU A 496 " pdb=" CG GLU A 496 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB GLU B 3 " pdb=" CG GLU B 3 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CB GLU A 358 " pdb=" CG GLU A 358 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 ... (remaining 9723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12953 1.81 - 3.62: 175 3.62 - 5.43: 23 5.43 - 7.24: 6 7.24 - 9.05: 1 Bond angle restraints: 13158 Sorted by residual: angle pdb=" C PHE A 483 " pdb=" CA PHE A 483 " pdb=" CB PHE A 483 " ideal model delta sigma weight residual 111.22 115.60 -4.38 1.24e+00 6.50e-01 1.25e+01 angle pdb=" N HIS A 338 " pdb=" CA HIS A 338 " pdb=" C HIS A 338 " ideal model delta sigma weight residual 113.16 109.36 3.80 1.24e+00 6.50e-01 9.38e+00 angle pdb=" CA GLU A 496 " pdb=" CB GLU A 496 " pdb=" CG GLU A 496 " ideal model delta sigma weight residual 114.10 120.08 -5.98 2.00e+00 2.50e-01 8.95e+00 angle pdb=" CA GLU B 3 " pdb=" CB GLU B 3 " pdb=" CG GLU B 3 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.01e+00 angle pdb=" CA LEU A 177 " pdb=" CB LEU A 177 " pdb=" CG LEU A 177 " ideal model delta sigma weight residual 116.30 125.35 -9.05 3.50e+00 8.16e-02 6.69e+00 ... (remaining 13153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5013 17.34 - 34.68: 644 34.68 - 52.02: 169 52.02 - 69.36: 35 69.36 - 86.71: 17 Dihedral angle restraints: 5878 sinusoidal: 2414 harmonic: 3464 Sorted by residual: dihedral pdb=" CA ILE A 262 " pdb=" C ILE A 262 " pdb=" N LEU A 263 " pdb=" CA LEU A 263 " ideal model delta harmonic sigma weight residual -180.00 -149.84 -30.16 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA PRO B 252 " pdb=" C PRO B 252 " pdb=" N PHE B 253 " pdb=" CA PHE B 253 " ideal model delta harmonic sigma weight residual 180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PHE B 101 " pdb=" C PHE B 101 " pdb=" N HIS B 102 " pdb=" CA HIS B 102 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 868 0.028 - 0.057: 395 0.057 - 0.085: 127 0.085 - 0.113: 80 0.113 - 0.142: 17 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CA ILE A 362 " pdb=" N ILE A 362 " pdb=" C ILE A 362 " pdb=" CB ILE A 362 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 361 " pdb=" N ILE B 361 " pdb=" C ILE B 361 " pdb=" CB ILE B 361 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE B 395 " pdb=" N ILE B 395 " pdb=" C ILE B 395 " pdb=" CB ILE B 395 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1484 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 483 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C PHE A 483 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 483 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A 484 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 437 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ASP A 437 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP A 437 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 438 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 662 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO B 663 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 663 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 663 " -0.025 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 180 2.67 - 3.23: 9218 3.23 - 3.79: 14903 3.79 - 4.34: 20474 4.34 - 4.90: 33331 Nonbonded interactions: 78106 Sorted by model distance: nonbonded pdb=" O LEU B 655 " pdb=" OG SER B 659 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR B 678 " pdb=" OD1 ASP B 716 " model vdw 2.187 3.040 nonbonded pdb=" O LEU B 615 " pdb=" OG1 THR B 619 " model vdw 2.206 3.040 nonbonded pdb=" O LEU B 29 " pdb=" OG SER B 35 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 223 " pdb=" O ASP A 225 " model vdw 2.247 3.040 ... (remaining 78101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.003 0.032 9728 Z= 0.127 Angle : 0.541 9.051 13158 Z= 0.295 Chirality : 0.041 0.142 1487 Planarity : 0.004 0.045 1690 Dihedral : 16.952 86.705 3628 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.66 % Allowed : 24.17 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1172 helix: 0.80 (0.22), residues: 579 sheet: -1.32 (0.41), residues: 155 loop : -1.24 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.014 0.001 TYR A 24 PHE 0.018 0.001 PHE A 455 TRP 0.020 0.001 TRP A 67 HIS 0.010 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9728) covalent geometry : angle 0.54144 (13158) hydrogen bonds : bond 0.14949 ( 431) hydrogen bonds : angle 6.38925 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.7364 (m100) cc_final: 0.6930 (m100) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.0955 time to fit residues: 15.6542 Evaluate side-chains 114 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 559 ASN B 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.190421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143794 restraints weight = 11036.872| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.42 r_work: 0.3489 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9728 Z= 0.131 Angle : 0.502 7.169 13158 Z= 0.269 Chirality : 0.042 0.145 1487 Planarity : 0.004 0.049 1690 Dihedral : 4.705 36.535 1302 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.02 % Allowed : 21.15 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.25), residues: 1172 helix: 0.92 (0.22), residues: 596 sheet: -1.36 (0.41), residues: 155 loop : -1.25 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.014 0.001 TYR B 700 PHE 0.020 0.001 PHE B 210 TRP 0.012 0.001 TRP A 303 HIS 0.005 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9728) covalent geometry : angle 0.50151 (13158) hydrogen bonds : bond 0.03965 ( 431) hydrogen bonds : angle 4.90460 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.324 Fit side-chains REVERT: A 270 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7135 (tmm) REVERT: A 489 LYS cc_start: 0.8248 (ptpp) cc_final: 0.7893 (mmtm) REVERT: B 41 ASP cc_start: 0.7935 (t70) cc_final: 0.7539 (m-30) REVERT: B 209 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6202 (mp0) outliers start: 32 outliers final: 16 residues processed: 138 average time/residue: 0.0946 time to fit residues: 18.1843 Evaluate side-chains 116 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.190054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137501 restraints weight = 11104.705| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.77 r_work: 0.3464 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9728 Z= 0.119 Angle : 0.478 7.448 13158 Z= 0.254 Chirality : 0.041 0.152 1487 Planarity : 0.004 0.048 1690 Dihedral : 4.569 39.309 1295 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.97 % Allowed : 20.49 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.25), residues: 1172 helix: 0.98 (0.22), residues: 603 sheet: -1.39 (0.41), residues: 155 loop : -1.30 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.010 0.001 TYR B 700 PHE 0.037 0.001 PHE A 483 TRP 0.011 0.001 TRP A 303 HIS 0.005 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9728) covalent geometry : angle 0.47823 (13158) hydrogen bonds : bond 0.03554 ( 431) hydrogen bonds : angle 4.59311 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.340 Fit side-chains REVERT: A 166 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: A 177 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 489 LYS cc_start: 0.8173 (ptpp) cc_final: 0.7878 (mmtm) REVERT: B 209 GLU cc_start: 0.6343 (mm-30) cc_final: 0.6122 (mp0) REVERT: B 314 LYS cc_start: 0.8483 (pttt) cc_final: 0.8164 (ptmm) REVERT: B 422 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7174 (m-70) outliers start: 42 outliers final: 26 residues processed: 148 average time/residue: 0.0851 time to fit residues: 17.9213 Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 104 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.187240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140738 restraints weight = 11240.508| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.44 r_work: 0.3446 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9728 Z= 0.173 Angle : 0.517 7.945 13158 Z= 0.272 Chirality : 0.042 0.149 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.694 38.000 1295 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 4.25 % Allowed : 21.34 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.25), residues: 1172 helix: 0.90 (0.22), residues: 600 sheet: -1.49 (0.41), residues: 155 loop : -1.26 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.010 0.001 TYR A 24 PHE 0.020 0.002 PHE A 483 TRP 0.009 0.001 TRP A 67 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9728) covalent geometry : angle 0.51681 (13158) hydrogen bonds : bond 0.03848 ( 431) hydrogen bonds : angle 4.63122 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.352 Fit side-chains REVERT: A 166 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 177 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 483 PHE cc_start: 0.8059 (p90) cc_final: 0.7802 (p90) REVERT: A 485 ASP cc_start: 0.7803 (m-30) cc_final: 0.7573 (m-30) REVERT: A 489 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7934 (mmtm) REVERT: B 41 ASP cc_start: 0.8028 (t70) cc_final: 0.7580 (m-30) REVERT: B 84 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8344 (p0) REVERT: B 209 GLU cc_start: 0.6515 (mm-30) cc_final: 0.6153 (mp0) REVERT: B 314 LYS cc_start: 0.8685 (pttt) cc_final: 0.8360 (ptmm) REVERT: B 422 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6992 (m-70) outliers start: 45 outliers final: 30 residues processed: 152 average time/residue: 0.0994 time to fit residues: 21.3691 Evaluate side-chains 137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.189114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142752 restraints weight = 11157.201| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.47 r_work: 0.3470 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9728 Z= 0.128 Angle : 0.495 7.813 13158 Z= 0.260 Chirality : 0.041 0.148 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.677 45.137 1295 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 4.53 % Allowed : 22.00 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.25), residues: 1172 helix: 1.03 (0.22), residues: 600 sheet: -1.51 (0.41), residues: 155 loop : -1.26 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.009 0.001 TYR B 700 PHE 0.015 0.001 PHE A 483 TRP 0.011 0.001 TRP A 303 HIS 0.010 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9728) covalent geometry : angle 0.49545 (13158) hydrogen bonds : bond 0.03433 ( 431) hydrogen bonds : angle 4.45325 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.249 Fit side-chains REVERT: A 166 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: A 177 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 489 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7866 (mmtm) REVERT: B 41 ASP cc_start: 0.7711 (t70) cc_final: 0.7442 (m-30) REVERT: B 209 GLU cc_start: 0.6251 (mm-30) cc_final: 0.6049 (mp0) REVERT: B 314 LYS cc_start: 0.8554 (pttt) cc_final: 0.8262 (ptmm) REVERT: B 422 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.7027 (m-70) outliers start: 48 outliers final: 32 residues processed: 158 average time/residue: 0.0929 time to fit residues: 20.7707 Evaluate side-chains 141 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.186398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140039 restraints weight = 11110.509| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.43 r_work: 0.3430 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9728 Z= 0.189 Angle : 0.553 12.095 13158 Z= 0.285 Chirality : 0.043 0.157 1487 Planarity : 0.004 0.045 1690 Dihedral : 4.833 53.106 1295 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 4.34 % Allowed : 22.29 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.25), residues: 1172 helix: 0.88 (0.22), residues: 600 sheet: -1.58 (0.41), residues: 155 loop : -1.31 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.011 0.001 TYR A 24 PHE 0.019 0.002 PHE B 106 TRP 0.014 0.002 TRP A 67 HIS 0.009 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9728) covalent geometry : angle 0.55332 (13158) hydrogen bonds : bond 0.03874 ( 431) hydrogen bonds : angle 4.59543 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: A 177 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 489 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7858 (mmtm) REVERT: B 41 ASP cc_start: 0.7895 (t70) cc_final: 0.7560 (m-30) REVERT: B 84 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8262 (p0) REVERT: B 314 LYS cc_start: 0.8584 (pttt) cc_final: 0.8301 (ptmm) REVERT: B 422 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6943 (m-70) outliers start: 46 outliers final: 32 residues processed: 138 average time/residue: 0.1015 time to fit residues: 19.4929 Evaluate side-chains 135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 24 optimal weight: 0.0030 chunk 110 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.188867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141730 restraints weight = 11153.816| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.48 r_work: 0.3448 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9728 Z= 0.147 Angle : 0.524 10.474 13158 Z= 0.272 Chirality : 0.042 0.155 1487 Planarity : 0.004 0.045 1690 Dihedral : 4.829 59.249 1295 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.68 % Allowed : 22.85 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.25), residues: 1172 helix: 0.95 (0.22), residues: 600 sheet: -1.54 (0.41), residues: 155 loop : -1.28 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.008 0.001 TYR B 700 PHE 0.017 0.001 PHE B 106 TRP 0.016 0.001 TRP A 67 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9728) covalent geometry : angle 0.52449 (13158) hydrogen bonds : bond 0.03523 ( 431) hydrogen bonds : angle 4.47557 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: A 177 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (mp) REVERT: A 270 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7316 (pmm) REVERT: A 489 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7874 (mmtm) REVERT: B 41 ASP cc_start: 0.7764 (t70) cc_final: 0.7466 (m-30) REVERT: B 52 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7985 (mtm180) REVERT: B 84 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8169 (p0) REVERT: B 314 LYS cc_start: 0.8603 (pttt) cc_final: 0.8310 (ptmm) REVERT: B 422 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7044 (m-70) outliers start: 39 outliers final: 28 residues processed: 133 average time/residue: 0.0986 time to fit residues: 18.5234 Evaluate side-chains 136 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.190843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143847 restraints weight = 10998.875| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.47 r_work: 0.3475 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9728 Z= 0.117 Angle : 0.512 9.505 13158 Z= 0.265 Chirality : 0.041 0.145 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.639 51.615 1295 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.78 % Allowed : 23.32 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.25), residues: 1172 helix: 1.08 (0.22), residues: 601 sheet: -1.51 (0.41), residues: 155 loop : -1.25 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.007 0.001 TYR B 700 PHE 0.017 0.001 PHE B 106 TRP 0.018 0.001 TRP A 67 HIS 0.012 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9728) covalent geometry : angle 0.51243 (13158) hydrogen bonds : bond 0.03208 ( 431) hydrogen bonds : angle 4.32206 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: A 177 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 270 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7147 (pmm) REVERT: A 489 LYS cc_start: 0.8131 (ptpp) cc_final: 0.7914 (mmtm) REVERT: B 52 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8021 (mtm180) REVERT: B 314 LYS cc_start: 0.8559 (pttt) cc_final: 0.8287 (ptmm) REVERT: B 347 PHE cc_start: 0.8151 (m-80) cc_final: 0.7925 (m-80) REVERT: B 422 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.7057 (m-70) outliers start: 40 outliers final: 28 residues processed: 143 average time/residue: 0.0925 time to fit residues: 18.6194 Evaluate side-chains 139 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.189816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144093 restraints weight = 11104.644| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.98 r_work: 0.3472 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9728 Z= 0.122 Angle : 0.525 9.019 13158 Z= 0.271 Chirality : 0.041 0.157 1487 Planarity : 0.004 0.045 1690 Dihedral : 4.557 46.627 1295 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 3.59 % Allowed : 23.42 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.25), residues: 1172 helix: 1.12 (0.22), residues: 600 sheet: -1.46 (0.41), residues: 155 loop : -1.23 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.007 0.001 TYR B 700 PHE 0.015 0.001 PHE B 106 TRP 0.020 0.001 TRP A 67 HIS 0.011 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9728) covalent geometry : angle 0.52483 (13158) hydrogen bonds : bond 0.03235 ( 431) hydrogen bonds : angle 4.29411 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: A 177 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 270 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7085 (pmm) REVERT: A 489 LYS cc_start: 0.8138 (ptpp) cc_final: 0.7934 (mmtm) REVERT: B 52 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7972 (mtm180) REVERT: B 314 LYS cc_start: 0.8511 (pttt) cc_final: 0.8196 (ptmm) REVERT: B 422 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.7019 (m-70) outliers start: 38 outliers final: 29 residues processed: 139 average time/residue: 0.0919 time to fit residues: 17.6060 Evaluate side-chains 139 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 0.2980 chunk 74 optimal weight: 0.0770 chunk 112 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.0060 chunk 19 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.192411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147265 restraints weight = 11119.038| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.95 r_work: 0.3520 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9728 Z= 0.102 Angle : 0.518 8.820 13158 Z= 0.267 Chirality : 0.041 0.163 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.391 40.399 1295 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 24.17 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 1172 helix: 1.24 (0.22), residues: 601 sheet: -1.40 (0.41), residues: 155 loop : -1.22 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.007 0.001 TYR B 700 PHE 0.016 0.001 PHE B 106 TRP 0.021 0.001 TRP A 67 HIS 0.010 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9728) covalent geometry : angle 0.51769 (13158) hydrogen bonds : bond 0.02949 ( 431) hydrogen bonds : angle 4.16867 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.296 Fit side-chains REVERT: A 166 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: B 52 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (mtm180) REVERT: B 210 PHE cc_start: 0.6553 (t80) cc_final: 0.6281 (t80) REVERT: B 314 LYS cc_start: 0.8478 (pttt) cc_final: 0.8205 (ptmm) REVERT: B 422 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6982 (m-70) outliers start: 30 outliers final: 22 residues processed: 134 average time/residue: 0.0923 time to fit residues: 17.5134 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 261 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 568 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 32 optimal weight: 0.0070 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.191135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145372 restraints weight = 11076.220| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.43 r_work: 0.3517 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9728 Z= 0.119 Angle : 0.528 8.719 13158 Z= 0.273 Chirality : 0.041 0.164 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.244 40.838 1292 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.74 % Allowed : 24.27 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1172 helix: 1.18 (0.22), residues: 604 sheet: -1.36 (0.42), residues: 155 loop : -1.21 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.007 0.001 TYR B 700 PHE 0.010 0.001 PHE B 205 TRP 0.038 0.002 TRP A 67 HIS 0.010 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9728) covalent geometry : angle 0.52809 (13158) hydrogen bonds : bond 0.03147 ( 431) hydrogen bonds : angle 4.21115 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.07 seconds wall clock time: 42 minutes 6.65 seconds (2526.65 seconds total)