Starting phenix.real_space_refine on Fri Jan 17 23:34:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo3_39434/01_2025/8yo3_39434.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo3_39434/01_2025/8yo3_39434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yo3_39434/01_2025/8yo3_39434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo3_39434/01_2025/8yo3_39434.map" model { file = "/net/cci-nas-00/data/ceres_data/8yo3_39434/01_2025/8yo3_39434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo3_39434/01_2025/8yo3_39434.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.077 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 42 5.16 5 C 7360 2.51 5 N 1948 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11514 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "C" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2194 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "D" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2194 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Time building chain proxies: 6.53, per 1000 atoms: 0.57 Number of scatterers: 11514 At special positions: 0 Unit cell: (108, 147, 113, 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 42 16.00 O 2164 8.00 N 1948 7.00 C 7360 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: 2.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 20 sheets defined 46.4% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 removed outlier: 3.631A pdb=" N SER A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.505A pdb=" N ASN A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.611A pdb=" N VAL A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.690A pdb=" N ASN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 removed outlier: 3.594A pdb=" N TYR A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.856A pdb=" N GLY A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 Processing helix chain 'A' and resid 239 through 254 removed outlier: 4.205A pdb=" N ASP A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 319 through 366 removed outlier: 3.608A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 427 Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.588A pdb=" N ASP A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 4.118A pdb=" N LEU C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP C 425 " --> pdb=" O GLY C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 455 through 466 Processing helix chain 'C' and resid 509 through 514 removed outlier: 3.500A pdb=" N LYS C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 Processing helix chain 'C' and resid 528 through 534 Processing helix chain 'C' and resid 559 through 564 Processing helix chain 'C' and resid 565 through 575 removed outlier: 4.060A pdb=" N SER C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.757A pdb=" N GLU C 582 " --> pdb=" O PRO C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 616 removed outlier: 4.588A pdb=" N ASP C 616 " --> pdb=" O GLU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 removed outlier: 3.561A pdb=" N SER C 631 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 632 " --> pdb=" O LEU C 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 628 through 632' Processing helix chain 'C' and resid 633 through 643 Processing helix chain 'C' and resid 654 through 662 removed outlier: 3.594A pdb=" N LEU C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 659 " --> pdb=" O TRP C 655 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 37 through 51 removed outlier: 3.516A pdb=" N PHE B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 75 through 89 removed outlier: 4.302A pdb=" N SER B 79 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.702A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.859A pdb=" N GLY B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.511A pdb=" N LEU B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 319 through 366 removed outlier: 3.532A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.940A pdb=" N SER B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 404 through 427 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.569A pdb=" N ASP B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'D' and resid 420 through 427 removed outlier: 4.075A pdb=" N ASP D 425 " --> pdb=" O GLY D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 removed outlier: 3.563A pdb=" N CYS D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 removed outlier: 3.525A pdb=" N LYS D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'D' and resid 528 through 534 Processing helix chain 'D' and resid 559 through 564 removed outlier: 3.620A pdb=" N GLY D 564 " --> pdb=" O HIS D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.064A pdb=" N SER D 569 " --> pdb=" O SER D 565 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 3.627A pdb=" N GLU D 582 " --> pdb=" O PRO D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 616 removed outlier: 4.659A pdb=" N ASP D 616 " --> pdb=" O GLU D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 632 removed outlier: 3.591A pdb=" N SER D 631 " --> pdb=" O GLY D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 643 Processing helix chain 'D' and resid 654 through 662 removed outlier: 3.534A pdb=" N PHE D 659 " --> pdb=" O TRP D 655 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.404A pdb=" N LEU C 411 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 555 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU C 413 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.384A pdb=" N ILE A 305 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 474 through 476 removed outlier: 6.847A pdb=" N GLU C 475 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 490 through 495 Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 508 Processing sheet with id=AB1, first strand: chain 'C' and resid 604 through 605 removed outlier: 3.712A pdb=" N ILE C 595 " --> pdb=" O ARG C 624 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 624 " --> pdb=" O ILE C 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.613A pdb=" N GLN B 2 " --> pdb=" O TYR D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'B' and resid 207 through 211 Processing sheet with id=AB6, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AB7, first strand: chain 'B' and resid 305 through 308 removed outlier: 4.315A pdb=" N ILE B 305 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 411 through 414 removed outlier: 6.246A pdb=" N LEU D 411 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET D 555 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU D 413 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 490 through 495 Processing sheet with id=AC1, first strand: chain 'D' and resid 505 through 508 Processing sheet with id=AC2, first strand: chain 'D' and resid 594 through 595 473 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3724 1.34 - 1.46: 1766 1.46 - 1.57: 6182 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 11750 Sorted by residual: bond pdb=" C TYR D 567 " pdb=" N PRO D 568 " ideal model delta sigma weight residual 1.336 1.350 -0.014 9.80e-03 1.04e+04 2.05e+00 bond pdb=" CB ASP A 70 " pdb=" CG ASP A 70 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.29e+00 bond pdb=" CA ASP A 70 " pdb=" CB ASP A 70 " ideal model delta sigma weight residual 1.528 1.546 -0.017 1.56e-02 4.11e+03 1.23e+00 bond pdb=" C TYR C 567 " pdb=" N PRO C 568 " ideal model delta sigma weight residual 1.337 1.348 -0.012 1.06e-02 8.90e+03 1.19e+00 bond pdb=" CB LYS A 9 " pdb=" CG LYS A 9 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 11745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 15675 2.43 - 4.86: 124 4.86 - 7.29: 22 7.29 - 9.72: 4 9.72 - 12.15: 1 Bond angle restraints: 15826 Sorted by residual: angle pdb=" CB LYS A 9 " pdb=" CG LYS A 9 " pdb=" CD LYS A 9 " ideal model delta sigma weight residual 111.30 119.79 -8.49 2.30e+00 1.89e-01 1.36e+01 angle pdb=" CA LEU B 395 " pdb=" CB LEU B 395 " pdb=" CG LEU B 395 " ideal model delta sigma weight residual 116.30 128.45 -12.15 3.50e+00 8.16e-02 1.21e+01 angle pdb=" N ILE C 420 " pdb=" CA ILE C 420 " pdb=" C ILE C 420 " ideal model delta sigma weight residual 113.07 108.43 4.64 1.36e+00 5.41e-01 1.16e+01 angle pdb=" CA MET C 447 " pdb=" CB MET C 447 " pdb=" CG MET C 447 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" C SER D 565 " pdb=" N ILE D 566 " pdb=" CA ILE D 566 " ideal model delta sigma weight residual 121.97 126.78 -4.81 1.80e+00 3.09e-01 7.14e+00 ... (remaining 15821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6046 17.85 - 35.70: 803 35.70 - 53.56: 195 53.56 - 71.41: 32 71.41 - 89.26: 16 Dihedral angle restraints: 7092 sinusoidal: 2928 harmonic: 4164 Sorted by residual: dihedral pdb=" CA GLY A 366 " pdb=" C GLY A 366 " pdb=" N GLU A 367 " pdb=" CA GLU A 367 " ideal model delta harmonic sigma weight residual -180.00 -156.07 -23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLY B 366 " pdb=" C GLY B 366 " pdb=" N GLU B 367 " pdb=" CA GLU B 367 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR B 238 " pdb=" C TYR B 238 " pdb=" N ASP B 239 " pdb=" CA ASP B 239 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 7089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1273 0.040 - 0.080: 308 0.080 - 0.120: 121 0.120 - 0.159: 8 0.159 - 0.199: 2 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CG LEU D 431 " pdb=" CB LEU D 431 " pdb=" CD1 LEU D 431 " pdb=" CD2 LEU D 431 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU C 431 " pdb=" CB LEU C 431 " pdb=" CD1 LEU C 431 " pdb=" CD2 LEU C 431 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA ILE A 29 " pdb=" N ILE A 29 " pdb=" C ILE A 29 " pdb=" CB ILE A 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1709 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 17 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C LEU A 17 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A 17 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 18 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 359 " -0.009 2.00e-02 2.50e+03 1.37e-02 3.26e+00 pdb=" CG PHE B 359 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 359 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 359 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 359 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 359 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 359 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 360 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ILE B 360 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B 360 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 361 " 0.010 2.00e-02 2.50e+03 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 477 2.72 - 3.27: 11771 3.27 - 3.81: 19018 3.81 - 4.36: 23177 4.36 - 4.90: 39116 Nonbonded interactions: 93559 Sorted by model distance: nonbonded pdb=" O ASN D 654 " pdb=" ND2 ASN D 654 " model vdw 2.177 3.120 nonbonded pdb=" O ASN C 654 " pdb=" ND2 ASN C 654 " model vdw 2.183 3.120 nonbonded pdb=" O GLY D 572 " pdb=" OG SER D 575 " model vdw 2.195 3.040 nonbonded pdb=" O ILE B 153 " pdb=" OH TYR B 434 " model vdw 2.215 3.040 nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 236 " model vdw 2.218 3.040 ... (remaining 93554 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.002 0.033 11750 Z= 0.157 Angle : 0.570 12.152 15826 Z= 0.298 Chirality : 0.040 0.199 1712 Planarity : 0.003 0.035 2026 Dihedral : 16.911 89.260 4420 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.73 % Allowed : 24.11 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1422 helix: 0.54 (0.23), residues: 564 sheet: -0.61 (0.41), residues: 190 loop : -0.04 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 655 HIS 0.008 0.001 HIS B 358 PHE 0.031 0.001 PHE B 359 TYR 0.016 0.001 TYR C 422 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 297 LEU cc_start: 0.7715 (mm) cc_final: 0.7463 (tp) REVERT: A 398 MET cc_start: 0.7872 (mtm) cc_final: 0.7666 (mtp) outliers start: 9 outliers final: 4 residues processed: 179 average time/residue: 0.2175 time to fit residues: 58.5029 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 176 HIS ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN B 176 HIS D 536 ASN D 642 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.166882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117487 restraints weight = 16481.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120998 restraints weight = 9676.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123257 restraints weight = 7105.492| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11750 Z= 0.196 Angle : 0.554 7.674 15826 Z= 0.295 Chirality : 0.042 0.164 1712 Planarity : 0.003 0.044 2026 Dihedral : 5.137 57.310 1560 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.74 % Allowed : 21.77 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1422 helix: 0.52 (0.22), residues: 582 sheet: -1.21 (0.39), residues: 170 loop : -0.03 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 655 HIS 0.006 0.001 HIS B 288 PHE 0.025 0.001 PHE B 350 TYR 0.016 0.001 TYR C 422 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8037 (mp10) cc_final: 0.7765 (mp10) REVERT: C 431 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8210 (pp) REVERT: C 517 MET cc_start: 0.1168 (ppp) cc_final: 0.0105 (pmm) REVERT: B 380 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7890 (tp30) REVERT: D 417 ASP cc_start: 0.7714 (t70) cc_final: 0.7423 (t70) outliers start: 34 outliers final: 17 residues processed: 207 average time/residue: 0.2137 time to fit residues: 66.2721 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 497 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.165328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115972 restraints weight = 16855.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119466 restraints weight = 9796.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121576 restraints weight = 7149.812| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11750 Z= 0.220 Angle : 0.528 7.446 15826 Z= 0.280 Chirality : 0.041 0.148 1712 Planarity : 0.003 0.049 2026 Dihedral : 4.678 36.161 1552 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.90 % Allowed : 21.13 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1422 helix: 0.61 (0.22), residues: 582 sheet: -1.51 (0.38), residues: 174 loop : -0.04 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 655 HIS 0.004 0.001 HIS B 288 PHE 0.019 0.001 PHE D 573 TYR 0.015 0.001 TYR C 422 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8065 (mp10) cc_final: 0.7778 (mp10) REVERT: A 265 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 431 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8398 (pp) REVERT: C 517 MET cc_start: 0.1652 (ppp) cc_final: 0.0476 (pmm) REVERT: C 547 MET cc_start: 0.8443 (mmm) cc_final: 0.8137 (mtt) REVERT: B 123 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.9018 (p) REVERT: B 190 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: B 380 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7908 (tp30) outliers start: 36 outliers final: 24 residues processed: 202 average time/residue: 0.2097 time to fit residues: 64.2594 Evaluate side-chains 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 50 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 0.1980 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 26 ASN A 81 GLN ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123900 restraints weight = 17029.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123976 restraints weight = 9831.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123878 restraints weight = 8164.219| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11750 Z= 0.170 Angle : 0.512 7.158 15826 Z= 0.269 Chirality : 0.041 0.151 1712 Planarity : 0.003 0.049 2026 Dihedral : 4.610 36.489 1552 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.55 % Allowed : 20.56 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1422 helix: 0.72 (0.22), residues: 580 sheet: -1.93 (0.40), residues: 150 loop : -0.02 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 655 HIS 0.003 0.001 HIS B 288 PHE 0.016 0.001 PHE B 350 TYR 0.013 0.001 TYR C 422 ARG 0.004 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8193 (mp10) cc_final: 0.7946 (mp10) REVERT: A 17 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6370 (mt) REVERT: A 265 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 431 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8374 (pp) REVERT: C 547 MET cc_start: 0.8336 (mmm) cc_final: 0.8132 (mtt) REVERT: B 87 MET cc_start: 0.8365 (mtt) cc_final: 0.8005 (mtt) REVERT: B 190 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: B 380 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7900 (tp30) REVERT: D 417 ASP cc_start: 0.7547 (t70) cc_final: 0.7265 (t70) outliers start: 44 outliers final: 28 residues processed: 210 average time/residue: 0.2143 time to fit residues: 68.0097 Evaluate side-chains 197 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 81 GLN C 497 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124769 restraints weight = 16843.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124611 restraints weight = 9457.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.124989 restraints weight = 7914.062| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11750 Z= 0.172 Angle : 0.512 7.103 15826 Z= 0.268 Chirality : 0.041 0.161 1712 Planarity : 0.003 0.051 2026 Dihedral : 4.590 36.850 1552 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.47 % Allowed : 20.97 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1422 helix: 0.74 (0.22), residues: 580 sheet: -1.87 (0.41), residues: 148 loop : 0.01 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 655 HIS 0.004 0.001 HIS B 288 PHE 0.018 0.001 PHE B 350 TYR 0.019 0.001 TYR D 422 ARG 0.003 0.000 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8215 (mp10) cc_final: 0.7929 (mp10) REVERT: A 265 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6924 (tm-30) REVERT: A 370 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8305 (m) REVERT: C 431 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8476 (pp) REVERT: C 445 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5915 (m100) REVERT: C 517 MET cc_start: 0.1987 (ppp) cc_final: -0.0090 (ptt) REVERT: C 583 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7724 (tp40) REVERT: C 659 PHE cc_start: 0.6927 (m-80) cc_final: 0.6500 (m-80) REVERT: B 190 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8116 (mt0) REVERT: B 265 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6951 (tm-30) REVERT: B 380 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7883 (tp30) REVERT: D 417 ASP cc_start: 0.7569 (t70) cc_final: 0.7317 (t70) outliers start: 43 outliers final: 28 residues processed: 208 average time/residue: 0.2359 time to fit residues: 75.8812 Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 115 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 19 optimal weight: 0.0030 chunk 129 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 81 GLN C 642 GLN B 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.168125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120352 restraints weight = 17273.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121178 restraints weight = 10141.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123088 restraints weight = 7703.767| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11750 Z= 0.211 Angle : 0.536 6.829 15826 Z= 0.280 Chirality : 0.042 0.178 1712 Planarity : 0.003 0.052 2026 Dihedral : 4.623 36.691 1552 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.55 % Allowed : 21.53 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1422 helix: 0.75 (0.22), residues: 582 sheet: -1.91 (0.41), residues: 150 loop : 0.00 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 655 HIS 0.005 0.001 HIS B 288 PHE 0.021 0.001 PHE C 573 TYR 0.014 0.001 TYR A 135 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8144 (mp10) cc_final: 0.7841 (mp10) REVERT: A 265 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 370 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8310 (m) REVERT: C 431 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8551 (pp) REVERT: C 445 TRP cc_start: 0.6862 (OUTLIER) cc_final: 0.5905 (m100) REVERT: C 517 MET cc_start: 0.1960 (ppp) cc_final: -0.0140 (ptt) REVERT: C 583 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7844 (tp40) REVERT: C 659 PHE cc_start: 0.7021 (m-80) cc_final: 0.6569 (m-80) REVERT: B 190 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: B 265 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 380 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7934 (tp30) REVERT: B 413 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7935 (mt-10) REVERT: D 417 ASP cc_start: 0.7621 (t70) cc_final: 0.7333 (t70) outliers start: 44 outliers final: 29 residues processed: 203 average time/residue: 0.2077 time to fit residues: 64.2056 Evaluate side-chains 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 9.9990 chunk 104 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 108 optimal weight: 0.0270 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 81 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114422 restraints weight = 17206.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118084 restraints weight = 9777.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120402 restraints weight = 7119.518| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11750 Z= 0.260 Angle : 0.567 8.627 15826 Z= 0.293 Chirality : 0.042 0.204 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.723 35.864 1552 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.55 % Allowed : 21.94 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1422 helix: 0.75 (0.22), residues: 580 sheet: -1.91 (0.41), residues: 150 loop : 0.04 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 655 HIS 0.004 0.001 HIS B 288 PHE 0.021 0.002 PHE D 605 TYR 0.015 0.001 TYR C 611 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8170 (mp10) cc_final: 0.7828 (mp10) REVERT: A 17 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.6557 (mt) REVERT: A 265 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 431 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8620 (pp) REVERT: C 445 TRP cc_start: 0.6774 (OUTLIER) cc_final: 0.5858 (m100) REVERT: C 517 MET cc_start: 0.2008 (ppp) cc_final: -0.0187 (ptt) REVERT: C 583 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7838 (tp40) REVERT: C 605 PHE cc_start: 0.8823 (m-10) cc_final: 0.8569 (m-10) REVERT: C 659 PHE cc_start: 0.6884 (m-80) cc_final: 0.6524 (m-80) REVERT: B 190 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: B 265 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 380 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7930 (tp30) REVERT: B 410 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8528 (ttpp) REVERT: B 413 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7881 (mt-10) REVERT: D 417 ASP cc_start: 0.7748 (t70) cc_final: 0.7445 (t70) outliers start: 44 outliers final: 33 residues processed: 201 average time/residue: 0.2164 time to fit residues: 65.0671 Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 82 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN B 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.168059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121117 restraints weight = 17141.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121951 restraints weight = 9661.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122555 restraints weight = 7475.726| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11750 Z= 0.172 Angle : 0.542 8.981 15826 Z= 0.280 Chirality : 0.041 0.207 1712 Planarity : 0.003 0.052 2026 Dihedral : 4.671 34.429 1552 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.39 % Allowed : 22.18 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1422 helix: 0.75 (0.22), residues: 580 sheet: -1.85 (0.41), residues: 150 loop : 0.06 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 655 HIS 0.004 0.000 HIS B 288 PHE 0.024 0.001 PHE D 605 TYR 0.011 0.001 TYR C 611 ARG 0.007 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8019 (mp10) cc_final: 0.7491 (mp10) REVERT: A 17 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6625 (mt) REVERT: A 265 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 431 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8586 (pp) REVERT: C 445 TRP cc_start: 0.6856 (OUTLIER) cc_final: 0.5961 (m100) REVERT: C 517 MET cc_start: 0.1852 (ppp) cc_final: -0.0332 (ptt) REVERT: C 583 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7841 (tp40) REVERT: C 605 PHE cc_start: 0.8730 (m-10) cc_final: 0.8522 (m-10) REVERT: C 659 PHE cc_start: 0.6905 (m-80) cc_final: 0.6482 (m-80) REVERT: B 190 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: B 265 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 380 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8001 (tp30) REVERT: B 410 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8512 (ttpp) REVERT: B 413 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7867 (mt-10) REVERT: D 417 ASP cc_start: 0.7661 (t70) cc_final: 0.7379 (t70) outliers start: 42 outliers final: 33 residues processed: 207 average time/residue: 0.2133 time to fit residues: 66.3612 Evaluate side-chains 210 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 55 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.163619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112216 restraints weight = 17278.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115763 restraints weight = 9983.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117960 restraints weight = 7355.481| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11750 Z= 0.344 Angle : 0.636 10.238 15826 Z= 0.328 Chirality : 0.043 0.231 1712 Planarity : 0.004 0.054 2026 Dihedral : 4.860 34.491 1552 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.31 % Allowed : 22.74 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1422 helix: 0.68 (0.22), residues: 582 sheet: -2.23 (0.43), residues: 130 loop : -0.04 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 445 HIS 0.005 0.001 HIS B 288 PHE 0.028 0.002 PHE D 605 TYR 0.027 0.002 TYR C 435 ARG 0.005 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8189 (mp10) cc_final: 0.7610 (mp10) REVERT: A 9 LYS cc_start: 0.8625 (tppt) cc_final: 0.8416 (tppt) REVERT: A 17 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.6714 (mt) REVERT: A 265 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7141 (tm-30) REVERT: C 431 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8603 (pp) REVERT: C 517 MET cc_start: 0.1718 (ppp) cc_final: -0.0363 (ptt) REVERT: C 583 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7756 (tp-100) REVERT: C 605 PHE cc_start: 0.8874 (m-10) cc_final: 0.8563 (m-10) REVERT: C 647 ASP cc_start: 0.8203 (t70) cc_final: 0.7643 (t0) REVERT: B 190 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 265 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 380 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7938 (tp30) outliers start: 41 outliers final: 34 residues processed: 197 average time/residue: 0.2134 time to fit residues: 63.3434 Evaluate side-chains 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 28 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 81 GLN ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN B 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.167368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116426 restraints weight = 17079.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120213 restraints weight = 9751.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122566 restraints weight = 7100.131| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11750 Z= 0.187 Angle : 0.583 8.792 15826 Z= 0.299 Chirality : 0.042 0.243 1712 Planarity : 0.003 0.053 2026 Dihedral : 4.781 38.627 1552 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.31 % Allowed : 22.98 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1422 helix: 0.77 (0.22), residues: 582 sheet: -1.88 (0.42), residues: 150 loop : 0.01 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 655 HIS 0.003 0.001 HIS B 288 PHE 0.032 0.002 PHE A 359 TYR 0.023 0.001 TYR C 435 ARG 0.008 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8058 (mp10) cc_final: 0.7511 (mp10) REVERT: A 9 LYS cc_start: 0.8624 (tppt) cc_final: 0.8420 (tppt) REVERT: A 17 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.6704 (mt) REVERT: A 265 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 431 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8566 (pp) REVERT: C 517 MET cc_start: 0.1705 (ppp) cc_final: -0.0315 (ptt) REVERT: C 605 PHE cc_start: 0.8798 (m-10) cc_final: 0.8514 (m-10) REVERT: C 647 ASP cc_start: 0.8167 (t70) cc_final: 0.7603 (t70) REVERT: B 190 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: B 265 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7072 (tm-30) REVERT: B 300 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7661 (mtm-85) REVERT: B 380 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7915 (tp30) REVERT: B 413 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7855 (mt-10) REVERT: D 417 ASP cc_start: 0.7752 (t70) cc_final: 0.7445 (t70) outliers start: 41 outliers final: 33 residues processed: 205 average time/residue: 0.2401 time to fit residues: 73.9606 Evaluate side-chains 206 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 91 optimal weight: 0.0070 chunk 31 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN D 432 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125835 restraints weight = 16856.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125231 restraints weight = 9503.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126047 restraints weight = 7919.871| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11750 Z= 0.167 Angle : 0.564 8.500 15826 Z= 0.289 Chirality : 0.041 0.228 1712 Planarity : 0.003 0.052 2026 Dihedral : 4.707 47.878 1552 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.82 % Allowed : 23.79 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1422 helix: 0.92 (0.23), residues: 568 sheet: -1.77 (0.42), residues: 150 loop : 0.04 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 655 HIS 0.003 0.000 HIS B 288 PHE 0.028 0.001 PHE A 359 TYR 0.023 0.001 TYR C 435 ARG 0.008 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.09 seconds wall clock time: 67 minutes 53.84 seconds (4073.84 seconds total)