Starting phenix.real_space_refine on Wed Apr 30 12:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zue_60482/04_2025/8zue_60482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zue_60482/04_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_60482/04_2025/8zue_60482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zue_60482/04_2025/8zue_60482.map" model { file = "/net/cci-nas-00/data/ceres_data/8zue_60482/04_2025/8zue_60482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zue_60482/04_2025/8zue_60482.cif" } resolution = 3.1 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.03, per 1000 atoms: 0.63 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.13 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: 3.39 Time building geometry restraints manager: 3.13 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.100 Find NCS groups from input model: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- 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 (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: -0.40 (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 TRP 0.020 0.001 TRP A 67 HIS 0.010 0.001 HIS A 283 PHE 0.018 0.001 PHE A 455 TYR 0.014 0.001 TYR A 24 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.14949 ( 431) hydrogen bonds : angle 6.38925 ( 1254) covalent geometry : bond 0.00280 ( 9728) covalent geometry : angle 0.54144 (13158) *********************** 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 : 0.952 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: 0.2815 time to fit residues: 46.4053 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 : 1.174 ------------------------------------------------------------------------------- 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 99 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 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 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 = 0.4244 r_free = 0.4244 target = 0.190684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144048 restraints weight = 10964.997| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.88 r_work: 0.3483 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0784 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= 0.126 Angle : 0.499 7.173 13158 Z= 0.267 Chirality : 0.042 0.145 1487 Planarity : 0.004 0.049 1690 Dihedral : 4.694 37.045 1302 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.12 % Allowed : 21.06 % 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 (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: -0.27 (0.25), residues: 1172 helix: 0.94 (0.22), residues: 596 sheet: -1.37 (0.41), residues: 155 loop : -1.26 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 303 HIS 0.006 0.001 HIS A 283 PHE 0.019 0.001 PHE B 210 TYR 0.013 0.001 TYR B 700 ARG 0.002 0.000 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 431) hydrogen bonds : angle 4.86069 ( 1254) covalent geometry : bond 0.00285 ( 9728) covalent geometry : angle 0.49856 (13158) *********************** 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 145 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 270 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6983 (tmm) REVERT: A 489 LYS cc_start: 0.8209 (ptpp) cc_final: 0.7886 (mmtm) REVERT: B 41 ASP cc_start: 0.7668 (t70) cc_final: 0.7387 (m-30) outliers start: 33 outliers final: 16 residues processed: 139 average time/residue: 0.3180 time to fit residues: 63.9415 Evaluate side-chains 113 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 5 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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** A 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.191600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139295 restraints weight = 11150.814| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.80 r_work: 0.3484 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9728 Z= 0.102 Angle : 0.465 7.434 13158 Z= 0.247 Chirality : 0.041 0.149 1487 Planarity : 0.004 0.049 1690 Dihedral : 4.514 40.502 1295 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 3.87 % Allowed : 20.68 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.17 (0.25), residues: 1172 helix: 1.05 (0.22), residues: 603 sheet: -1.35 (0.41), residues: 155 loop : -1.29 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 303 HIS 0.006 0.001 HIS A 283 PHE 0.034 0.001 PHE A 483 TYR 0.010 0.001 TYR B 700 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 431) hydrogen bonds : angle 4.52041 ( 1254) covalent geometry : bond 0.00224 ( 9728) covalent geometry : angle 0.46519 (13158) *********************** 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 156 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.966 Fit side-chains REVERT: A 166 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: A 177 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 489 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7863 (mmtm) REVERT: B 209 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5966 (mp0) REVERT: B 422 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.7131 (m-70) outliers start: 41 outliers final: 21 residues processed: 146 average time/residue: 0.2121 time to fit residues: 44.1440 Evaluate side-chains 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 263 LEU Chi-restraints excluded: chain A residue 267 ARG 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 568 VAL Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.191839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.145420 restraints weight = 11025.324| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.42 r_work: 0.3524 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9728 Z= 0.103 Angle : 0.464 7.611 13158 Z= 0.245 Chirality : 0.040 0.144 1487 Planarity : 0.004 0.048 1690 Dihedral : 4.225 37.344 1292 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.49 % Allowed : 21.06 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.06 (0.25), residues: 1172 helix: 1.15 (0.22), residues: 601 sheet: -1.32 (0.41), residues: 155 loop : -1.23 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 303 HIS 0.005 0.001 HIS A 283 PHE 0.023 0.001 PHE A 483 TYR 0.010 0.001 TYR A 24 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 431) hydrogen bonds : angle 4.36639 ( 1254) covalent geometry : bond 0.00232 ( 9728) covalent geometry : angle 0.46436 (13158) *********************** 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 155 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 1.473 Fit side-chains REVERT: A 166 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: A 489 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7810 (mmtm) REVERT: B 314 LYS cc_start: 0.8455 (pttt) cc_final: 0.8195 (ptmm) REVERT: B 422 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.7089 (m-70) outliers start: 37 outliers final: 23 residues processed: 145 average time/residue: 0.2291 time to fit residues: 47.1614 Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 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 503 ILE Chi-restraints excluded: chain A residue 523 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.191740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147221 restraints weight = 11051.150| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.78 r_work: 0.3520 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1334 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= 0.105 Angle : 0.473 7.631 13158 Z= 0.248 Chirality : 0.041 0.142 1487 Planarity : 0.004 0.047 1690 Dihedral : 4.188 38.053 1292 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.68 % Allowed : 22.00 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.02 (0.25), residues: 1172 helix: 1.25 (0.22), residues: 600 sheet: -1.31 (0.41), residues: 155 loop : -1.22 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 67 HIS 0.005 0.001 HIS A 283 PHE 0.021 0.001 PHE B 106 TYR 0.008 0.001 TYR B 700 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 431) hydrogen bonds : angle 4.26815 ( 1254) covalent geometry : bond 0.00241 ( 9728) covalent geometry : angle 0.47285 (13158) *********************** 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 153 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.097 Fit side-chains REVERT: A 166 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: A 489 LYS cc_start: 0.8074 (ptpp) cc_final: 0.7807 (mmtm) REVERT: B 314 LYS cc_start: 0.8455 (pttt) cc_final: 0.8185 (ptmm) REVERT: B 422 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.7050 (m-70) outliers start: 39 outliers final: 27 residues processed: 143 average time/residue: 0.2194 time to fit residues: 44.4983 Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 166 GLU 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 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 503 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 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 33 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 0.0020 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.191199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138781 restraints weight = 11091.171| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.81 r_work: 0.3479 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1375 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= 0.115 Angle : 0.498 11.041 13158 Z= 0.256 Chirality : 0.041 0.140 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.202 38.590 1292 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 3.40 % Allowed : 22.47 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.03 (0.25), residues: 1172 helix: 1.26 (0.22), residues: 600 sheet: -1.34 (0.41), residues: 155 loop : -1.21 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 67 HIS 0.008 0.001 HIS A 283 PHE 0.014 0.001 PHE B 106 TYR 0.008 0.001 TYR B 700 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 431) hydrogen bonds : angle 4.23944 ( 1254) covalent geometry : bond 0.00267 ( 9728) covalent geometry : angle 0.49812 (13158) *********************** 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 146 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.173 Fit side-chains REVERT: A 166 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: A 489 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7815 (mmtm) REVERT: B 314 LYS cc_start: 0.8485 (pttt) cc_final: 0.8159 (ptmm) REVERT: B 422 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.7047 (m-70) outliers start: 36 outliers final: 27 residues processed: 137 average time/residue: 0.2216 time to fit residues: 43.3873 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 149 LEU 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 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 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 472 SER 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 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 49 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.190755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144852 restraints weight = 11133.641| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.41 r_work: 0.3517 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1439 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= 0.119 Angle : 0.497 10.477 13158 Z= 0.256 Chirality : 0.041 0.167 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.233 39.442 1292 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 3.68 % Allowed : 22.29 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.02 (0.25), residues: 1172 helix: 1.25 (0.22), residues: 600 sheet: -1.39 (0.41), residues: 155 loop : -1.20 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 67 HIS 0.008 0.001 HIS A 283 PHE 0.018 0.001 PHE B 365 TYR 0.011 0.001 TYR A 24 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 431) hydrogen bonds : angle 4.23225 ( 1254) covalent geometry : bond 0.00279 ( 9728) covalent geometry : angle 0.49709 (13158) *********************** 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 148 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: A 489 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7831 (mmtm) REVERT: B 52 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7988 (mtm180) REVERT: B 234 ASN cc_start: 0.7657 (t0) cc_final: 0.7333 (t0) REVERT: B 314 LYS cc_start: 0.8472 (pttt) cc_final: 0.8198 (ptmm) REVERT: B 422 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6976 (m-70) outliers start: 39 outliers final: 30 residues processed: 140 average time/residue: 0.2306 time to fit residues: 45.5643 Evaluate side-chains 141 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 166 GLU 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 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET 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 443 LEU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.189462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143082 restraints weight = 11219.988| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.44 r_work: 0.3469 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1487 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= 0.141 Angle : 0.514 9.285 13158 Z= 0.266 Chirality : 0.042 0.170 1487 Planarity : 0.004 0.045 1690 Dihedral : 4.299 40.334 1292 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 3.49 % Allowed : 22.76 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.25), residues: 1172 helix: 1.16 (0.22), residues: 603 sheet: -1.45 (0.41), residues: 155 loop : -1.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 67 HIS 0.011 0.001 HIS A 283 PHE 0.015 0.001 PHE B 365 TYR 0.007 0.001 TYR B 700 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 431) hydrogen bonds : angle 4.30202 ( 1254) covalent geometry : bond 0.00335 ( 9728) covalent geometry : angle 0.51396 (13158) *********************** 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 145 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 1.041 Fit side-chains REVERT: A 166 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: A 489 LYS cc_start: 0.8102 (ptpp) cc_final: 0.7843 (mmtm) REVERT: B 41 ASP cc_start: 0.7708 (t70) cc_final: 0.7427 (m-30) REVERT: B 314 LYS cc_start: 0.8512 (pttt) cc_final: 0.8210 (ptmm) REVERT: B 422 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6998 (m-70) outliers start: 37 outliers final: 30 residues processed: 139 average time/residue: 0.2156 time to fit residues: 42.2656 Evaluate side-chains 135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 166 GLU 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 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET 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 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 Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 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 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 = 0.4238 r_free = 0.4238 target = 0.190398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144517 restraints weight = 11071.438| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.96 r_work: 0.3475 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9728 Z= 0.120 Angle : 0.509 8.835 13158 Z= 0.264 Chirality : 0.041 0.173 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.293 40.638 1292 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.31 % Allowed : 23.32 % 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 (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: -0.06 (0.25), residues: 1172 helix: 1.18 (0.22), residues: 603 sheet: -1.45 (0.41), residues: 155 loop : -1.24 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 67 HIS 0.010 0.001 HIS A 283 PHE 0.018 0.001 PHE B 365 TYR 0.028 0.001 TYR B 714 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 431) hydrogen bonds : angle 4.23311 ( 1254) covalent geometry : bond 0.00281 ( 9728) covalent geometry : angle 0.50906 (13158) *********************** 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 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: A 489 LYS cc_start: 0.8099 (ptpp) cc_final: 0.7887 (mmtm) REVERT: B 314 LYS cc_start: 0.8519 (pttt) cc_final: 0.8204 (ptmm) REVERT: B 422 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6994 (m-70) outliers start: 35 outliers final: 29 residues processed: 133 average time/residue: 0.2193 time to fit residues: 41.5939 Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 166 GLU 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 300 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 365 MET 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 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 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.190921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144741 restraints weight = 11197.859| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.48 r_work: 0.3494 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1618 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= 0.115 Angle : 0.520 8.530 13158 Z= 0.269 Chirality : 0.041 0.177 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.258 40.737 1292 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.21 % Allowed : 23.51 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.03 (0.25), residues: 1172 helix: 1.21 (0.22), residues: 603 sheet: -1.43 (0.41), residues: 155 loop : -1.24 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 67 HIS 0.010 0.001 HIS A 283 PHE 0.017 0.001 PHE B 365 TYR 0.027 0.001 TYR B 714 ARG 0.007 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 431) hydrogen bonds : angle 4.18640 ( 1254) covalent geometry : bond 0.00268 ( 9728) covalent geometry : angle 0.52041 (13158) ********************** 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: 34 poor density : 108 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.7197 (m100) cc_final: 0.6739 (m100) REVERT: A 166 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 489 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7881 (mmtm) REVERT: B 314 LYS cc_start: 0.8512 (pttt) cc_final: 0.8208 (ptmm) REVERT: B 422 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7006 (m-70) outliers start: 34 outliers final: 29 residues processed: 134 average time/residue: 0.2733 time to fit residues: 52.3779 Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 166 GLU 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 402 ASP Chi-restraints excluded: chain A residue 472 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.191929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146029 restraints weight = 11092.859| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.91 r_work: 0.3526 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1671 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= 0.110 Angle : 0.522 8.741 13158 Z= 0.269 Chirality : 0.041 0.180 1487 Planarity : 0.004 0.046 1690 Dihedral : 4.221 40.991 1292 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 3.02 % Allowed : 23.70 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.25), residues: 1172 helix: 1.25 (0.22), residues: 604 sheet: -1.39 (0.41), residues: 155 loop : -1.22 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 67 HIS 0.012 0.001 HIS A 283 PHE 0.017 0.001 PHE B 365 TYR 0.026 0.001 TYR B 714 ARG 0.005 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.02987 ( 431) hydrogen bonds : angle 4.13213 ( 1254) covalent geometry : bond 0.00254 ( 9728) covalent geometry : angle 0.52161 (13158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5554.87 seconds wall clock time: 99 minutes 47.65 seconds (5987.65 seconds total)