Starting phenix.real_space_refine on Sat Jun 7 09:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wiu_32536/06_2025/7wiu_32536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiu_32536/06_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_32536/06_2025/7wiu_32536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiu_32536/06_2025/7wiu_32536.map" model { file = "/net/cci-nas-00/data/ceres_data/7wiu_32536/06_2025/7wiu_32536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiu_32536/06_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-5710/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: 6.74, per 1000 atoms: 0.78 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 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: 2.38 Time building geometry restraints manager: 2.91 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: 4.420 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.110 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- 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= 0.270 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 Details of bonding type rmsd hydrogen bonds : bond 0.13410 ( 480) hydrogen bonds : angle 5.42524 ( 1431) covalent geometry : bond 0.00443 ( 8778) covalent geometry : angle 0.94132 (11991) *********************** 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 : 1.002 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: 0.2101 time to fit residues: 47.3611 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 : 0.928 ------------------------------------------------------------------------------- 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 = 0.096414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082401 restraints weight = 21968.199| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.99 r_work: 0.3113 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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= 0.182 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 Details of bonding type rmsd hydrogen bonds : bond 0.06148 ( 480) hydrogen bonds : angle 4.57019 ( 1431) covalent geometry : bond 0.00392 ( 8778) covalent geometry : angle 0.75295 (11991) *********************** 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 : 0.897 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5551 (OUTLIER) cc_final: 0.5001 (m-10) REVERT: A 392 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8625 (tmtt) REVERT: A 515 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8743 (mtmm) REVERT: A 518 MET cc_start: 0.8640 (ttm) cc_final: 0.8411 (tpp) REVERT: A 582 HIS cc_start: 0.8577 (t70) cc_final: 0.8211 (t-170) REVERT: B 22 LEU cc_start: 0.9084 (tt) cc_final: 0.8730 (mm) REVERT: B 48 GLU cc_start: 0.8446 (pp20) cc_final: 0.8115 (pp20) REVERT: B 123 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8411 (mp0) REVERT: B 280 MET cc_start: 0.8668 (mmt) cc_final: 0.8444 (mmt) REVERT: B 411 VAL cc_start: 0.9502 (t) cc_final: 0.9297 (p) REVERT: B 492 LEU cc_start: 0.9246 (pp) cc_final: 0.8976 (pp) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.1955 time to fit residues: 36.6335 Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 0.0470 chunk 24 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084402 restraints weight = 21643.352| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.96 r_work: 0.3211 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 0.046 8778 Z= 0.131 Angle : 0.691 10.068 11991 Z= 0.342 Chirality : 0.042 0.181 1462 Planarity : 0.005 0.049 1536 Dihedral : 5.835 52.172 1255 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.71 % Favored : 89.94 % Rotamer: Outliers : 3.30 % Allowed : 17.27 % Favored : 79.43 % 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: -1.15 (0.25), residues: 1143 helix: 0.76 (0.20), residues: 722 sheet: -2.64 (0.74), residues: 40 loop : -3.69 (0.26), residues: 381 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 A 329 Details of bonding type rmsd hydrogen bonds : bond 0.05296 ( 480) hydrogen bonds : angle 4.16509 ( 1431) covalent geometry : bond 0.00258 ( 8778) covalent geometry : angle 0.69136 (11991) *********************** 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 163 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5629 (OUTLIER) cc_final: 0.5053 (m-10) REVERT: A 316 GLU cc_start: 0.8268 (tp30) cc_final: 0.8036 (tp30) REVERT: A 392 LYS cc_start: 0.9033 (tmmt) cc_final: 0.8717 (tmtt) REVERT: A 397 ASP cc_start: 0.8579 (m-30) cc_final: 0.8340 (m-30) REVERT: A 515 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8801 (mtmm) REVERT: A 582 HIS cc_start: 0.8574 (t70) cc_final: 0.8137 (t-170) REVERT: B 22 LEU cc_start: 0.9060 (tt) cc_final: 0.8734 (mm) REVERT: B 48 GLU cc_start: 0.8428 (pp20) cc_final: 0.8054 (pp20) REVERT: B 123 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8392 (mp0) REVERT: B 492 LEU cc_start: 0.9165 (pp) cc_final: 0.8927 (pp) outliers start: 29 outliers final: 13 residues processed: 152 average time/residue: 0.1608 time to fit residues: 36.4404 Evaluate side-chains 136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 436 VAL 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 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: 2.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.098118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084420 restraints weight = 21598.376| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.04 r_work: 0.3224 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8778 Z= 0.130 Angle : 0.676 9.501 11991 Z= 0.336 Chirality : 0.041 0.160 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.519 55.006 1253 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.89 % Favored : 89.76 % Rotamer: Outliers : 3.41 % Allowed : 19.77 % 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: -0.81 (0.26), residues: 1143 helix: 1.01 (0.20), residues: 723 sheet: -2.43 (0.75), residues: 40 loop : -3.53 (0.26), residues: 380 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 0.019 0.001 PHE A 559 TYR 0.016 0.001 TYR A 619 ARG 0.003 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 480) hydrogen bonds : angle 4.05461 ( 1431) covalent geometry : bond 0.00262 ( 8778) covalent geometry : angle 0.67619 (11991) *********************** 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 163 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5427 (OUTLIER) cc_final: 0.4887 (m-10) REVERT: A 392 LYS cc_start: 0.9039 (tmmt) cc_final: 0.8661 (tmtt) REVERT: A 514 LYS cc_start: 0.8008 (mptt) cc_final: 0.7542 (mttt) REVERT: A 515 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8774 (mtmm) REVERT: A 522 THR cc_start: 0.9076 (m) cc_final: 0.8846 (t) REVERT: A 582 HIS cc_start: 0.8634 (t70) cc_final: 0.8177 (t-170) REVERT: A 655 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9269 (tp) REVERT: B 22 LEU cc_start: 0.9092 (tt) cc_final: 0.8885 (mm) REVERT: B 29 VAL cc_start: 0.8985 (t) cc_final: 0.8737 (p) REVERT: B 48 GLU cc_start: 0.8463 (pp20) cc_final: 0.8074 (pp20) REVERT: B 123 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8350 (mp0) REVERT: B 186 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8305 (p0) outliers start: 30 outliers final: 16 residues processed: 151 average time/residue: 0.1788 time to fit residues: 38.8632 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 564 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 ASP 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 221 ASN Chi-restraints excluded: chain B residue 329 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: 3.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.098521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084831 restraints weight = 21431.047| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.04 r_work: 0.3237 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2158 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= 0.127 Angle : 0.679 9.616 11991 Z= 0.334 Chirality : 0.042 0.181 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.426 56.849 1253 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.36 % Favored : 90.29 % Rotamer: Outliers : 3.41 % Allowed : 20.57 % Favored : 76.02 % 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: -0.64 (0.26), residues: 1143 helix: 1.17 (0.20), residues: 719 sheet: -2.17 (0.79), residues: 38 loop : -3.50 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.002 0.000 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 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 480) hydrogen bonds : angle 3.97806 ( 1431) covalent geometry : bond 0.00254 ( 8778) covalent geometry : angle 0.67898 (11991) *********************** 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 158 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5459 (OUTLIER) cc_final: 0.4943 (m100) REVERT: A 514 LYS cc_start: 0.7999 (mptt) cc_final: 0.7540 (mttt) REVERT: A 515 LYS cc_start: 0.9209 (mtmm) cc_final: 0.8769 (mtmm) REVERT: A 522 THR cc_start: 0.9031 (m) cc_final: 0.8812 (t) REVERT: A 655 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9284 (tp) REVERT: B 48 GLU cc_start: 0.8421 (pp20) cc_final: 0.8037 (pp20) REVERT: B 123 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8296 (mp0) REVERT: B 130 ASN cc_start: 0.9292 (m-40) cc_final: 0.9034 (m-40) REVERT: B 186 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (p0) outliers start: 30 outliers final: 19 residues processed: 147 average time/residue: 0.1664 time to fit residues: 35.8037 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 : 0.993 ------------------------------------------------------------------------------- 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 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 645 SER Chi-restraints excluded: chain A residue 655 LEU 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 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 329 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.096630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084484 restraints weight = 21701.174| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.77 r_work: 0.3260 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2320 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= 0.128 Angle : 0.673 10.791 11991 Z= 0.332 Chirality : 0.042 0.158 1462 Planarity : 0.005 0.055 1536 Dihedral : 5.361 58.409 1253 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.19 % Favored : 90.46 % Rotamer: Outliers : 3.41 % Allowed : 21.59 % Favored : 75.00 % 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: -0.50 (0.26), residues: 1143 helix: 1.33 (0.21), residues: 709 sheet: -1.83 (0.83), residues: 38 loop : -3.48 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.003 0.000 HIS A 582 PHE 0.015 0.001 PHE A 559 TYR 0.014 0.001 TYR A 619 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 480) hydrogen bonds : angle 3.95064 ( 1431) covalent geometry : bond 0.00260 ( 8778) covalent geometry : angle 0.67331 (11991) *********************** 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 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5516 (OUTLIER) cc_final: 0.5012 (m100) REVERT: A 514 LYS cc_start: 0.8004 (mptt) cc_final: 0.7601 (mttt) REVERT: A 515 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8907 (mtmm) REVERT: A 522 THR cc_start: 0.8968 (m) cc_final: 0.8751 (t) REVERT: A 655 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9280 (tp) REVERT: B 48 GLU cc_start: 0.8349 (pp20) cc_final: 0.7976 (pp20) REVERT: B 123 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8258 (mp0) REVERT: B 130 ASN cc_start: 0.9215 (m-40) cc_final: 0.8963 (m-40) REVERT: B 186 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8273 (p0) outliers start: 30 outliers final: 21 residues processed: 142 average time/residue: 0.1739 time to fit residues: 36.1166 Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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 655 LEU 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 221 ASN 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: 5.9990 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.098538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084516 restraints weight = 22112.428| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.02 r_work: 0.3238 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2306 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= 0.163 Angle : 0.691 10.507 11991 Z= 0.344 Chirality : 0.043 0.151 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.411 58.822 1253 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.27 % Favored : 90.38 % Rotamer: Outliers : 3.64 % Allowed : 22.05 % 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: -0.51 (0.26), residues: 1143 helix: 1.33 (0.21), residues: 709 sheet: -1.68 (0.84), residues: 38 loop : -3.52 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 529 HIS 0.014 0.001 HIS A 582 PHE 0.010 0.001 PHE A 775 TYR 0.014 0.001 TYR A 619 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.05200 ( 480) hydrogen bonds : angle 4.04969 ( 1431) covalent geometry : bond 0.00356 ( 8778) covalent geometry : angle 0.69124 (11991) *********************** 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 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.000 Fit side-chains REVERT: A 277 TRP cc_start: 0.5449 (OUTLIER) cc_final: 0.4979 (m100) REVERT: A 514 LYS cc_start: 0.8060 (mptt) cc_final: 0.7621 (mttt) REVERT: A 522 THR cc_start: 0.9019 (m) cc_final: 0.8796 (t) REVERT: B 48 GLU cc_start: 0.8384 (pp20) cc_final: 0.8006 (pp20) REVERT: B 123 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8304 (mp0) REVERT: B 130 ASN cc_start: 0.9233 (m-40) cc_final: 0.8963 (m-40) REVERT: B 186 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8323 (p0) outliers start: 32 outliers final: 24 residues processed: 142 average time/residue: 0.1855 time to fit residues: 37.8986 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 357 VAL 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 570 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 THR 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 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: 0.0570 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085613 restraints weight = 22337.703| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.07 r_work: 0.3174 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8778 Z= 0.137 Angle : 0.697 11.402 11991 Z= 0.341 Chirality : 0.042 0.200 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.377 59.613 1253 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.36 % Favored : 90.38 % Rotamer: Outliers : 3.64 % Allowed : 21.93 % Favored : 74.43 % 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: -0.43 (0.26), residues: 1143 helix: 1.40 (0.21), residues: 709 sheet: -1.54 (0.89), residues: 38 loop : -3.50 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.005 0.000 HIS B 569 PHE 0.021 0.001 PHE A 559 TYR 0.013 0.001 TYR A 619 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 480) hydrogen bonds : angle 3.97680 ( 1431) covalent geometry : bond 0.00284 ( 8778) covalent geometry : angle 0.69662 (11991) *********************** 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 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.950 Fit side-chains REVERT: A 277 TRP cc_start: 0.5347 (OUTLIER) cc_final: 0.4935 (m100) REVERT: A 514 LYS cc_start: 0.8016 (mptt) cc_final: 0.7561 (mttt) REVERT: A 522 THR cc_start: 0.9010 (m) cc_final: 0.8792 (t) REVERT: B 48 GLU cc_start: 0.8396 (pp20) cc_final: 0.7993 (pp20) REVERT: B 123 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8355 (mp0) REVERT: B 130 ASN cc_start: 0.9255 (m-40) cc_final: 0.8973 (m-40) REVERT: B 186 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8333 (p0) outliers start: 32 outliers final: 23 residues processed: 140 average time/residue: 0.1838 time to fit residues: 37.1580 Evaluate side-chains 141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 357 VAL 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 583 LEU Chi-restraints excluded: chain A residue 586 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.0570 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086997 restraints weight = 21952.449| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.04 r_work: 0.3253 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2560 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= 0.127 Angle : 0.694 12.582 11991 Z= 0.338 Chirality : 0.042 0.205 1462 Planarity : 0.005 0.055 1536 Dihedral : 5.262 58.216 1253 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.92 % Favored : 90.81 % Rotamer: Outliers : 2.84 % Allowed : 22.39 % Favored : 74.77 % 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: -0.31 (0.26), residues: 1143 helix: 1.48 (0.21), residues: 710 sheet: -1.48 (0.92), residues: 38 loop : -3.45 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.007 0.000 HIS B 569 PHE 0.008 0.001 PHE B 419 TYR 0.012 0.001 TYR A 619 ARG 0.005 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 480) hydrogen bonds : angle 3.88714 ( 1431) covalent geometry : bond 0.00256 ( 8778) covalent geometry : angle 0.69417 (11991) *********************** 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 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.004 Fit side-chains REVERT: A 277 TRP cc_start: 0.5268 (OUTLIER) cc_final: 0.4861 (m100) REVERT: A 514 LYS cc_start: 0.7995 (mptt) cc_final: 0.7548 (mttt) REVERT: A 515 LYS cc_start: 0.9253 (mtmm) cc_final: 0.8978 (mtmm) REVERT: B 48 GLU cc_start: 0.8385 (pp20) cc_final: 0.7986 (pp20) REVERT: B 123 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8218 (mp0) REVERT: B 130 ASN cc_start: 0.9249 (m-40) cc_final: 0.8971 (m-40) REVERT: B 186 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8297 (p0) outliers start: 25 outliers final: 20 residues processed: 140 average time/residue: 0.1985 time to fit residues: 40.8879 Evaluate side-chains 141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 478 GLU 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 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: 3.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.0020 chunk 57 optimal weight: 0.0010 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 0.0770 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086693 restraints weight = 21147.379| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.76 r_work: 0.3290 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8778 Z= 0.126 Angle : 0.709 13.369 11991 Z= 0.339 Chirality : 0.042 0.199 1462 Planarity : 0.005 0.056 1536 Dihedral : 5.130 56.641 1251 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.84 % Favored : 90.90 % Rotamer: Outliers : 2.84 % Allowed : 22.50 % Favored : 74.66 % 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: 1.55 (0.20), residues: 710 sheet: -1.43 (0.92), residues: 38 loop : -3.37 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.014 0.001 HIS B 569 PHE 0.017 0.001 PHE A 559 TYR 0.011 0.001 TYR B 283 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 480) hydrogen bonds : angle 3.80888 ( 1431) covalent geometry : bond 0.00249 ( 8778) covalent geometry : angle 0.70887 (11991) ********************** 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 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.001 Fit side-chains REVERT: A 277 TRP cc_start: 0.5291 (OUTLIER) cc_final: 0.4927 (m100) REVERT: A 514 LYS cc_start: 0.8064 (mptt) cc_final: 0.7656 (mttt) REVERT: A 515 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8961 (mtmm) REVERT: B 48 GLU cc_start: 0.8339 (pp20) cc_final: 0.7952 (pp20) REVERT: B 123 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8136 (mp0) REVERT: B 130 ASN cc_start: 0.9198 (m-40) cc_final: 0.8941 (m-40) REVERT: B 186 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8268 (p0) outliers start: 25 outliers final: 20 residues processed: 134 average time/residue: 0.2071 time to fit residues: 41.6724 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 478 GLU 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 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 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: 4.9990 chunk 57 optimal weight: 0.0670 chunk 100 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3593 r_free = 0.3593 target = 0.098149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084368 restraints weight = 21747.071| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.06 r_work: 0.3231 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2655 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= 0.146 Angle : 0.715 13.320 11991 Z= 0.346 Chirality : 0.043 0.203 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.154 56.612 1251 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.36 % Favored : 90.38 % 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: -0.23 (0.26), residues: 1143 helix: 1.53 (0.20), residues: 710 sheet: -1.35 (0.78), residues: 47 loop : -3.42 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.012 0.001 HIS B 569 PHE 0.009 0.001 PHE B 419 TYR 0.013 0.001 TYR B 283 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 480) hydrogen bonds : angle 3.91626 ( 1431) covalent geometry : bond 0.00318 ( 8778) covalent geometry : angle 0.71528 (11991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3921.11 seconds wall clock time: 69 minutes 44.96 seconds (4184.96 seconds total)