Starting phenix.real_space_refine on Thu Feb 13 03:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wiu_32536/02_2025/7wiu_32536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiu_32536/02_2025/7wiu_32536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wiu_32536/02_2025/7wiu_32536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiu_32536/02_2025/7wiu_32536.map" model { file = "/net/cci-nas-00/data/ceres_data/7wiu_32536/02_2025/7wiu_32536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiu_32536/02_2025/7wiu_32536.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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 14 5.16 5 C 5501 2.51 5 N 1547 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Time building chain proxies: 5.99, per 1000 atoms: 0.70 Number of scatterers: 8615 At special positions: 0 Unit cell: (70.52, 98.4, 136.12, 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 14 16.00 O 1553 8.00 N 1547 7.00 C 5501 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 65.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 309 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.837A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 375 removed outlier: 4.011A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.168A pdb=" N PHE A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.905A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 Proline residue: A 419 - end of helix removed outlier: 3.539A pdb=" N VAL A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 removed outlier: 4.263A pdb=" N ALA A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 457 through 479 Processing helix chain 'A' and resid 479 through 486 removed outlier: 3.869A pdb=" N ILE A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.809A pdb=" N PHE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.776A pdb=" N GLY A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 734 through 738 removed outlier: 3.517A pdb=" N ASP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 738 " --> pdb=" O GLY A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 738' Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.771A pdb=" N ARG A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 781 through 790 Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.817A pdb=" N ILE A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 832 Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'B' and resid 14 through 46 removed outlier: 3.524A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Proline residue: B 40 - end of helix removed outlier: 4.402A pdb=" N ALA B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.515A pdb=" N TRP B 104 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 105 " --> pdb=" O LEU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.703A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.634A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.510A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 153 through 202 removed outlier: 3.514A pdb=" N VAL B 158 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 4.947A pdb=" N ARG B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 removed outlier: 3.830A pdb=" N ARG B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.757A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.613A pdb=" N GLY B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.822A pdb=" N ILE B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.975A pdb=" N THR B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.529A pdb=" N THR B 374 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 472 through 486 removed outlier: 3.737A pdb=" N LYS B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.609A pdb=" N GLY B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.815A pdb=" N PHE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 668 through 669 removed outlier: 3.586A pdb=" N VAL A 669 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 672 " --> pdb=" O VAL A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689 Processing sheet with id=AA3, first strand: chain 'A' and resid 813 through 815 removed outlier: 3.868A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'B' and resid 537 through 540 removed outlier: 6.822A pdb=" N VAL B 537 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 548 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 539 " --> pdb=" O VAL B 546 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1407 1.32 - 1.44: 2237 1.44 - 1.56: 5111 1.56 - 1.68: 0 1.68 - 1.81: 23 Bond restraints: 8778 Sorted by residual: bond pdb=" C ILE B 392 " pdb=" O ILE B 392 " ideal model delta sigma weight residual 1.237 1.200 0.037 9.80e-03 1.04e+04 1.45e+01 bond pdb=" C PRO B 385 " pdb=" O PRO B 385 " ideal model delta sigma weight residual 1.233 1.192 0.041 1.13e-02 7.83e+03 1.33e+01 bond pdb=" N TYR A 619 " pdb=" CA TYR A 619 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.10e+00 bond pdb=" N TRP A 277 " pdb=" CA TRP A 277 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.49e+00 bond pdb=" N HIS A 614 " pdb=" CA HIS A 614 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.22e+00 ... (remaining 8773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11520 2.17 - 4.35: 393 4.35 - 6.52: 62 6.52 - 8.69: 13 8.69 - 10.86: 3 Bond angle restraints: 11991 Sorted by residual: angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 114.92 106.77 8.15 1.30e+00 5.92e-01 3.93e+01 angle pdb=" C ARG A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta sigma weight residual 119.84 127.52 -7.68 1.25e+00 6.40e-01 3.77e+01 angle pdb=" N PRO B 385 " pdb=" CA PRO B 385 " pdb=" C PRO B 385 " ideal model delta sigma weight residual 110.80 102.13 8.67 1.51e+00 4.39e-01 3.29e+01 angle pdb=" N ARG A 278 " pdb=" CA ARG A 278 " pdb=" C ARG A 278 " ideal model delta sigma weight residual 111.07 117.01 -5.94 1.07e+00 8.73e-01 3.08e+01 angle pdb=" C THR B 395 " pdb=" CA THR B 395 " pdb=" CB THR B 395 " ideal model delta sigma weight residual 113.45 102.59 10.86 1.98e+00 2.55e-01 3.01e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4701 17.97 - 35.94: 399 35.94 - 53.91: 82 53.91 - 71.88: 12 71.88 - 89.85: 7 Dihedral angle restraints: 5201 sinusoidal: 1940 harmonic: 3261 Sorted by residual: dihedral pdb=" CA ASP B 325 " pdb=" C ASP B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual 180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN B 11 " pdb=" C ASN B 11 " pdb=" N ASP B 12 " pdb=" CA ASP B 12 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" C TYR A 619 " pdb=" N TYR A 619 " pdb=" CA TYR A 619 " pdb=" CB TYR A 619 " ideal model delta harmonic sigma weight residual -122.60 -135.20 12.60 0 2.50e+00 1.60e-01 2.54e+01 ... (remaining 5198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1339 0.080 - 0.160: 107 0.160 - 0.240: 5 0.240 - 0.320: 5 0.320 - 0.400: 6 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CA TYR A 619 " pdb=" N TYR A 619 " pdb=" C TYR A 619 " pdb=" CB TYR A 619 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA PHE A 612 " pdb=" N PHE A 612 " pdb=" C PHE A 612 " pdb=" CB PHE A 612 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASP B 393 " pdb=" N ASP B 393 " pdb=" C ASP B 393 " pdb=" CB ASP B 393 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1459 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 326 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLY B 326 " 0.077 2.00e-02 2.50e+03 pdb=" O GLY B 326 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA B 327 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 14 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ARG B 14 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG B 14 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 15 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 842 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP A 842 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP A 842 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 843 " 0.016 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 113 2.64 - 3.20: 8427 3.20 - 3.77: 12631 3.77 - 4.33: 16378 4.33 - 4.90: 27125 Nonbonded interactions: 64674 Sorted by model distance: nonbonded pdb=" OG1 THR B 395 " pdb=" N ASP B 396 " model vdw 2.070 3.120 nonbonded pdb=" O ARG A 620 " pdb=" NE ARG A 620 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR A 826 " pdb=" OE1 GLU A 829 " model vdw 2.209 3.040 nonbonded pdb=" O ASP B 336 " pdb=" NH1 ARG B 387 " model vdw 2.218 3.120 nonbonded pdb=" NH2 ARG A 620 " pdb=" N GLY A 622 " model vdw 2.231 3.200 ... (remaining 64669 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8778 Z= 0.298 Angle : 0.941 10.863 11991 Z= 0.585 Chirality : 0.052 0.400 1462 Planarity : 0.005 0.044 1536 Dihedral : 14.542 89.849 3099 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.72 % Favored : 87.40 % Rotamer: Outliers : 2.16 % Allowed : 6.93 % Favored : 90.91 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.22), residues: 1143 helix: -1.09 (0.18), residues: 710 sheet: -3.65 (0.61), residues: 40 loop : -4.44 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 172 HIS 0.004 0.001 HIS B 383 PHE 0.027 0.001 PHE A 612 TYR 0.014 0.001 TYR A 619 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5109 (OUTLIER) cc_final: 0.4401 (m-10) REVERT: A 515 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8591 (mtmm) REVERT: A 548 ASN cc_start: 0.9062 (m110) cc_final: 0.8849 (m-40) REVERT: A 582 HIS cc_start: 0.8374 (t-90) cc_final: 0.8157 (t-170) REVERT: B 22 LEU cc_start: 0.9073 (tt) cc_final: 0.8727 (mm) REVERT: B 48 GLU cc_start: 0.7886 (pp20) cc_final: 0.7636 (pp20) REVERT: B 123 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8084 (mp0) REVERT: B 130 ASN cc_start: 0.9357 (m-40) cc_final: 0.9109 (m-40) REVERT: B 368 SER cc_start: 0.8517 (t) cc_final: 0.7588 (t) REVERT: B 387 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6319 (ptm-80) REVERT: B 389 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7642 (mtp85) REVERT: B 391 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 393 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7932 (p0) REVERT: B 411 VAL cc_start: 0.9503 (t) cc_final: 0.9268 (m) outliers start: 19 outliers final: 9 residues processed: 165 average time/residue: 0.2384 time to fit residues: 54.1801 Evaluate side-chains 128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 620 ARG Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 395 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 548 ASN A 582 HIS A 597 HIS ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 HIS B 109 ASN B 241 GLN B 405 GLN B 420 HIS B 504 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.096413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082400 restraints weight = 21968.657| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.99 r_work: 0.3190 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8778 Z= 0.260 Angle : 0.753 10.001 11991 Z= 0.380 Chirality : 0.044 0.174 1462 Planarity : 0.005 0.066 1536 Dihedral : 6.885 54.120 1277 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.94 % Favored : 88.89 % Rotamer: Outliers : 2.16 % Allowed : 16.02 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.25), residues: 1143 helix: 0.20 (0.20), residues: 713 sheet: -3.00 (0.70), residues: 40 loop : -3.93 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 172 HIS 0.004 0.001 HIS A 614 PHE 0.018 0.001 PHE A 612 TYR 0.019 0.002 TYR A 619 ARG 0.008 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5605 (OUTLIER) cc_final: 0.5059 (m-10) REVERT: A 392 LYS cc_start: 0.9005 (tmmt) cc_final: 0.8611 (tmtt) REVERT: A 515 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8744 (mtmm) REVERT: A 582 HIS cc_start: 0.8491 (t70) cc_final: 0.8150 (t-170) REVERT: B 22 LEU cc_start: 0.9102 (tt) cc_final: 0.8754 (mm) REVERT: B 48 GLU cc_start: 0.8400 (pp20) cc_final: 0.8078 (pp20) REVERT: B 123 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8375 (mp0) REVERT: B 280 MET cc_start: 0.8524 (mmt) cc_final: 0.8302 (mmt) REVERT: B 492 LEU cc_start: 0.9252 (pp) cc_final: 0.8997 (pp) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.1946 time to fit residues: 36.1493 Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 83 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 812 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085522 restraints weight = 21661.207| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.00 r_work: 0.3241 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8778 Z= 0.162 Angle : 0.691 9.923 11991 Z= 0.340 Chirality : 0.042 0.185 1462 Planarity : 0.005 0.049 1536 Dihedral : 5.772 52.815 1255 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.45 % Favored : 90.20 % Rotamer: Outliers : 3.64 % Allowed : 16.59 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.25), residues: 1143 helix: 0.80 (0.20), residues: 725 sheet: -2.90 (0.66), residues: 47 loop : -3.69 (0.26), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.002 0.000 HIS A 614 PHE 0.008 0.001 PHE B 564 TYR 0.019 0.001 TYR A 619 ARG 0.006 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5578 (OUTLIER) cc_final: 0.5003 (m-10) REVERT: A 392 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8712 (tmtt) REVERT: A 397 ASP cc_start: 0.8550 (m-30) cc_final: 0.8327 (m-30) REVERT: A 515 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8790 (mtmm) REVERT: A 522 THR cc_start: 0.9050 (m) cc_final: 0.8832 (t) REVERT: A 582 HIS cc_start: 0.8580 (t70) cc_final: 0.8123 (t-170) REVERT: B 22 LEU cc_start: 0.9060 (tt) cc_final: 0.8745 (mm) REVERT: B 48 GLU cc_start: 0.8435 (pp20) cc_final: 0.8057 (pp20) REVERT: B 123 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8377 (mp0) REVERT: B 149 LEU cc_start: 0.9383 (tp) cc_final: 0.9174 (tt) outliers start: 32 outliers final: 13 residues processed: 160 average time/residue: 0.1672 time to fit residues: 39.3114 Evaluate side-chains 135 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 812 GLN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082017 restraints weight = 21741.686| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.02 r_work: 0.3213 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8778 Z= 0.247 Angle : 0.704 9.579 11991 Z= 0.353 Chirality : 0.043 0.158 1462 Planarity : 0.005 0.052 1536 Dihedral : 5.614 54.245 1253 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.80 % Favored : 89.85 % Rotamer: Outliers : 3.75 % Allowed : 19.43 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.26), residues: 1143 helix: 0.93 (0.20), residues: 725 sheet: -2.51 (0.72), residues: 40 loop : -3.55 (0.26), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.002 0.001 HIS A 614 PHE 0.015 0.001 PHE A 559 TYR 0.017 0.002 TYR A 619 ARG 0.003 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5547 (OUTLIER) cc_final: 0.5022 (m-10) REVERT: A 392 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8781 (tmtt) REVERT: A 514 LYS cc_start: 0.8009 (mptt) cc_final: 0.7553 (mttt) REVERT: A 515 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8803 (mtmm) REVERT: A 529 TRP cc_start: 0.9201 (t60) cc_final: 0.8968 (t-100) REVERT: A 582 HIS cc_start: 0.8590 (t70) cc_final: 0.8148 (t-170) REVERT: B 22 LEU cc_start: 0.9127 (tt) cc_final: 0.8785 (mm) REVERT: B 48 GLU cc_start: 0.8422 (pp20) cc_final: 0.8052 (pp20) REVERT: B 123 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8326 (mp0) REVERT: B 186 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8332 (p0) outliers start: 33 outliers final: 21 residues processed: 147 average time/residue: 0.1779 time to fit residues: 37.9729 Evaluate side-chains 141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084636 restraints weight = 21420.601| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.03 r_work: 0.3234 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8778 Z= 0.166 Angle : 0.683 9.016 11991 Z= 0.337 Chirality : 0.042 0.173 1462 Planarity : 0.004 0.053 1536 Dihedral : 5.492 56.939 1253 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.36 % Favored : 90.29 % Rotamer: Outliers : 3.07 % Allowed : 21.48 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.26), residues: 1143 helix: 1.12 (0.20), residues: 723 sheet: -2.19 (0.75), residues: 40 loop : -3.47 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.008 0.001 HIS B 569 PHE 0.008 0.001 PHE B 419 TYR 0.015 0.001 TYR A 619 ARG 0.003 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5464 (OUTLIER) cc_final: 0.4953 (m100) REVERT: A 392 LYS cc_start: 0.9044 (tmmt) cc_final: 0.8764 (tmtt) REVERT: A 397 ASP cc_start: 0.8585 (m-30) cc_final: 0.8319 (m-30) REVERT: A 515 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8776 (mtmm) REVERT: A 522 THR cc_start: 0.9045 (m) cc_final: 0.8831 (t) REVERT: A 582 HIS cc_start: 0.8641 (t70) cc_final: 0.8177 (t-170) REVERT: B 48 GLU cc_start: 0.8441 (pp20) cc_final: 0.8044 (pp20) REVERT: B 123 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 156 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8870 (tp) REVERT: B 186 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8301 (p0) outliers start: 27 outliers final: 16 residues processed: 143 average time/residue: 0.1704 time to fit residues: 35.7868 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 45 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 0.0020 chunk 81 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087619 restraints weight = 21898.600| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.05 r_work: 0.3211 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8778 Z= 0.160 Angle : 0.677 9.828 11991 Z= 0.330 Chirality : 0.042 0.163 1462 Planarity : 0.004 0.055 1536 Dihedral : 5.348 58.851 1253 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.10 % Favored : 90.55 % Rotamer: Outliers : 2.73 % Allowed : 22.73 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.26), residues: 1143 helix: 1.38 (0.21), residues: 709 sheet: -1.80 (0.81), residues: 40 loop : -3.48 (0.26), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.008 0.000 HIS B 569 PHE 0.016 0.001 PHE A 559 TYR 0.013 0.001 TYR A 619 ARG 0.004 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5336 (OUTLIER) cc_final: 0.4887 (m100) REVERT: A 514 LYS cc_start: 0.7972 (mptt) cc_final: 0.7508 (mttt) REVERT: A 515 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8718 (mtmm) REVERT: A 582 HIS cc_start: 0.8695 (t70) cc_final: 0.8486 (t-170) REVERT: B 48 GLU cc_start: 0.8380 (pp20) cc_final: 0.7995 (pp20) REVERT: B 123 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8309 (mp0) REVERT: B 186 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8300 (p0) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.1855 time to fit residues: 38.8513 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086217 restraints weight = 22096.176| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.05 r_work: 0.3233 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8778 Z= 0.189 Angle : 0.687 10.830 11991 Z= 0.335 Chirality : 0.042 0.213 1462 Planarity : 0.004 0.054 1536 Dihedral : 5.338 59.843 1253 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.19 % Favored : 90.46 % Rotamer: Outliers : 3.41 % Allowed : 22.73 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.26), residues: 1143 helix: 1.42 (0.21), residues: 709 sheet: -1.61 (0.86), residues: 38 loop : -3.48 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 529 HIS 0.007 0.001 HIS B 569 PHE 0.009 0.001 PHE B 419 TYR 0.013 0.001 TYR A 619 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.002 Fit side-chains REVERT: A 277 TRP cc_start: 0.5410 (OUTLIER) cc_final: 0.4948 (m100) REVERT: A 514 LYS cc_start: 0.7996 (mptt) cc_final: 0.7560 (mttt) REVERT: B 48 GLU cc_start: 0.8387 (pp20) cc_final: 0.7995 (pp20) REVERT: B 123 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8308 (mp0) REVERT: B 186 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8289 (p0) outliers start: 30 outliers final: 21 residues processed: 142 average time/residue: 0.1880 time to fit residues: 38.0123 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.100638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086677 restraints weight = 22289.495| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.06 r_work: 0.3233 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8778 Z= 0.174 Angle : 0.689 11.915 11991 Z= 0.336 Chirality : 0.042 0.196 1462 Planarity : 0.004 0.054 1536 Dihedral : 5.288 59.249 1253 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.01 % Favored : 90.73 % Rotamer: Outliers : 3.64 % Allowed : 22.16 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.26), residues: 1143 helix: 1.45 (0.20), residues: 709 sheet: -1.49 (0.90), residues: 38 loop : -3.44 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.006 0.001 HIS B 569 PHE 0.009 0.001 PHE B 419 TYR 0.012 0.001 TYR A 444 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.904 Fit side-chains REVERT: A 277 TRP cc_start: 0.5363 (OUTLIER) cc_final: 0.4935 (m100) REVERT: A 514 LYS cc_start: 0.8008 (mptt) cc_final: 0.7553 (mttt) REVERT: B 48 GLU cc_start: 0.8356 (pp20) cc_final: 0.7957 (pp20) REVERT: B 123 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8286 (mp0) REVERT: B 186 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8279 (p0) outliers start: 32 outliers final: 23 residues processed: 144 average time/residue: 0.1901 time to fit residues: 39.2365 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 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 582 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086971 restraints weight = 21939.338| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.04 r_work: 0.3248 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8778 Z= 0.173 Angle : 0.704 12.695 11991 Z= 0.340 Chirality : 0.042 0.190 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.190 58.458 1251 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.84 % Favored : 90.90 % Rotamer: Outliers : 3.18 % Allowed : 22.50 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.26), residues: 1143 helix: 1.50 (0.20), residues: 709 sheet: -1.46 (0.91), residues: 38 loop : -3.38 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.017 0.001 HIS A 582 PHE 0.008 0.001 PHE B 419 TYR 0.012 0.001 TYR A 619 ARG 0.005 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.957 Fit side-chains REVERT: A 277 TRP cc_start: 0.5257 (OUTLIER) cc_final: 0.4854 (m100) REVERT: A 514 LYS cc_start: 0.8037 (mptt) cc_final: 0.7599 (mttt) REVERT: A 515 LYS cc_start: 0.9272 (mtmm) cc_final: 0.8986 (mtmm) REVERT: A 522 THR cc_start: 0.8959 (m) cc_final: 0.8749 (t) REVERT: B 48 GLU cc_start: 0.8358 (pp20) cc_final: 0.7956 (pp20) REVERT: B 123 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8242 (mp0) REVERT: B 186 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8289 (p0) outliers start: 28 outliers final: 22 residues processed: 137 average time/residue: 0.1801 time to fit residues: 35.7490 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087626 restraints weight = 21981.655| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.04 r_work: 0.3260 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8778 Z= 0.166 Angle : 0.707 13.191 11991 Z= 0.339 Chirality : 0.042 0.187 1462 Planarity : 0.004 0.054 1536 Dihedral : 5.134 57.219 1251 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.57 % Favored : 91.16 % Rotamer: Outliers : 2.84 % Allowed : 23.07 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.26), residues: 1143 helix: 1.54 (0.20), residues: 710 sheet: -1.42 (0.92), residues: 38 loop : -3.33 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.009 0.001 HIS B 569 PHE 0.008 0.001 PHE B 419 TYR 0.011 0.001 TYR B 283 ARG 0.004 0.000 ARG A 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.323 Fit side-chains REVERT: A 277 TRP cc_start: 0.5293 (OUTLIER) cc_final: 0.4931 (m100) REVERT: A 514 LYS cc_start: 0.8067 (mptt) cc_final: 0.7629 (mttt) REVERT: A 515 LYS cc_start: 0.9279 (mtmm) cc_final: 0.8985 (mtmm) REVERT: B 48 GLU cc_start: 0.8343 (pp20) cc_final: 0.7938 (pp20) REVERT: B 123 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8183 (mp0) REVERT: B 186 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8303 (p0) outliers start: 25 outliers final: 20 residues processed: 137 average time/residue: 0.1866 time to fit residues: 37.3381 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.0770 chunk 57 optimal weight: 0.0070 chunk 100 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 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 = 0.3620 r_free = 0.3620 target = 0.101727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087800 restraints weight = 22172.833| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.06 r_work: 0.3251 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8778 Z= 0.169 Angle : 0.721 13.123 11991 Z= 0.343 Chirality : 0.042 0.183 1462 Planarity : 0.004 0.054 1536 Dihedral : 5.109 56.332 1251 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.66 % Favored : 91.08 % Rotamer: Outliers : 2.73 % Allowed : 23.75 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.26), residues: 1143 helix: 1.58 (0.20), residues: 710 sheet: -1.37 (0.92), residues: 38 loop : -3.30 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.006 0.000 HIS B 569 PHE 0.008 0.001 PHE B 419 TYR 0.013 0.001 TYR A 444 ARG 0.003 0.000 ARG A 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.25 seconds wall clock time: 63 minutes 49.75 seconds (3829.75 seconds total)