Starting phenix.real_space_refine on Tue Jul 29 15:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo3_39434/07_2025/8yo3_39434.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo3_39434/07_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_39434/07_2025/8yo3_39434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo3_39434/07_2025/8yo3_39434.map" model { file = "/net/cci-nas-00/data/ceres_data/8yo3_39434/07_2025/8yo3_39434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo3_39434/07_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-5711/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: 9.39, per 1000 atoms: 0.82 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: 3.95 Conformation dependent library (CDL) restraints added in 2.8 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: 1.58 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: 5.80 Time building geometry restraints manager: 3.69 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: 83.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.160 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:4.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.830 ------------------------------------------------------------------------------- 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= 0.111 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 Details of bonding type rmsd hydrogen bonds : bond 0.22547 ( 473) hydrogen bonds : angle 8.03280 ( 1305) covalent geometry : bond 0.00237 (11750) covalent geometry : angle 0.56973 (15826) *********************** 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 : 1.356 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: 0.2935 time to fit residues: 79.7984 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 : 1.437 ------------------------------------------------------------------------------- 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 = 0.117493 restraints weight = 16481.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121034 restraints weight = 9666.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123152 restraints weight = 7102.721| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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= 0.131 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 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 473) hydrogen bonds : angle 5.50970 ( 1305) covalent geometry : bond 0.00296 (11750) covalent geometry : angle 0.55355 (15826) *********************** 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 : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8041 (mp10) cc_final: 0.7769 (mp10) REVERT: C 431 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8211 (pp) REVERT: C 517 MET cc_start: 0.1214 (ppp) cc_final: 0.0141 (pmm) REVERT: B 380 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7881 (tp30) REVERT: D 417 ASP cc_start: 0.7701 (t70) cc_final: 0.7414 (t70) outliers start: 34 outliers final: 17 residues processed: 207 average time/residue: 0.2588 time to fit residues: 80.5577 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 : 1.499 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 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: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.162215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112741 restraints weight = 16945.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116083 restraints weight = 9954.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118252 restraints weight = 7305.538| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11750 Z= 0.196 Angle : 0.567 7.589 15826 Z= 0.299 Chirality : 0.043 0.228 1712 Planarity : 0.003 0.051 2026 Dihedral : 4.810 36.308 1552 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.47 % Allowed : 20.40 % Favored : 76.13 % 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: -0.11 (0.23), residues: 1422 helix: 0.59 (0.22), residues: 580 sheet: -1.68 (0.41), residues: 158 loop : -0.09 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 655 HIS 0.005 0.001 HIS B 288 PHE 0.022 0.002 PHE B 359 TYR 0.019 0.002 TYR C 422 ARG 0.007 0.000 ARG B 6 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 473) hydrogen bonds : angle 5.22264 ( 1305) covalent geometry : bond 0.00458 (11750) covalent geometry : angle 0.56745 (15826) *********************** 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 219 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8154 (mp10) cc_final: 0.7846 (mp10) REVERT: A 17 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6460 (mt) REVERT: A 265 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7111 (tm-30) REVERT: C 431 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8432 (pp) REVERT: C 517 MET cc_start: 0.1665 (ppp) cc_final: 0.0517 (pmm) REVERT: C 547 MET cc_start: 0.8456 (mmm) cc_final: 0.8214 (mtt) REVERT: B 123 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9046 (p) REVERT: B 190 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: B 380 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7936 (tp30) REVERT: D 422 TYR cc_start: 0.8317 (m-80) cc_final: 0.8107 (m-10) outliers start: 43 outliers final: 26 residues processed: 204 average time/residue: 0.2471 time to fit residues: 75.6790 Evaluate side-chains 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 ILE 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 566 ILE 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 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 663 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 50 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115108 restraints weight = 16684.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118621 restraints weight = 9763.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120868 restraints weight = 7136.759| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11750 Z= 0.126 Angle : 0.524 7.323 15826 Z= 0.275 Chirality : 0.041 0.160 1712 Planarity : 0.003 0.050 2026 Dihedral : 4.716 36.324 1552 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.63 % Allowed : 20.73 % Favored : 75.65 % 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: -0.02 (0.23), residues: 1422 helix: 0.67 (0.22), residues: 582 sheet: -1.98 (0.41), residues: 150 loop : 0.01 (0.25), residues: 690 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 0.017 0.001 PHE D 605 TYR 0.014 0.001 TYR C 422 ARG 0.004 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 473) hydrogen bonds : angle 5.00360 ( 1305) covalent geometry : bond 0.00293 (11750) covalent geometry : angle 0.52411 (15826) *********************** 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 225 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8116 (mp10) cc_final: 0.7802 (mp10) REVERT: A 17 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6435 (mt) REVERT: A 265 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7064 (tm-30) REVERT: C 431 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8527 (pp) REVERT: C 517 MET cc_start: 0.2105 (ppp) cc_final: -0.0043 (ptt) REVERT: C 547 MET cc_start: 0.8363 (mmm) cc_final: 0.8119 (mtt) REVERT: B 123 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.9014 (p) REVERT: B 190 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: B 265 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 380 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7924 (tp30) REVERT: D 417 ASP cc_start: 0.7715 (t70) cc_final: 0.7403 (t70) REVERT: D 517 MET cc_start: 0.3543 (pmm) cc_final: 0.3240 (ppp) outliers start: 45 outliers final: 27 residues processed: 208 average time/residue: 0.3141 time to fit residues: 103.3520 Evaluate side-chains 201 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 134 GLU 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 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 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 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 629 LEU 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: 1.9990 chunk 59 optimal weight: 0.0870 chunk 96 optimal weight: 0.0770 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- 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 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN C 642 GLN D 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.169637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124547 restraints weight = 16901.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123960 restraints weight = 9706.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124198 restraints weight = 8286.894| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11750 Z= 0.104 Angle : 0.514 7.843 15826 Z= 0.269 Chirality : 0.041 0.171 1712 Planarity : 0.003 0.051 2026 Dihedral : 4.622 36.511 1552 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 21.85 % Favored : 75.00 % 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: 0.07 (0.23), residues: 1422 helix: 0.76 (0.22), residues: 580 sheet: -1.93 (0.41), residues: 150 loop : 0.05 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 655 HIS 0.004 0.000 HIS B 288 PHE 0.018 0.001 PHE D 605 TYR 0.015 0.001 TYR D 422 ARG 0.002 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 473) hydrogen bonds : angle 4.86138 ( 1305) covalent geometry : bond 0.00236 (11750) covalent geometry : angle 0.51395 (15826) *********************** 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 224 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8229 (mp10) cc_final: 0.7924 (mp10) REVERT: A 265 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 370 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8346 (m) REVERT: C 422 TYR cc_start: 0.8028 (m-80) cc_final: 0.7786 (m-10) REVERT: C 431 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8544 (pp) REVERT: C 445 TRP cc_start: 0.6796 (OUTLIER) cc_final: 0.5852 (m100) REVERT: C 517 MET cc_start: 0.1891 (ppp) cc_final: -0.0222 (ptt) REVERT: C 583 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7897 (tp40) REVERT: C 659 PHE cc_start: 0.7026 (m-80) cc_final: 0.6569 (m-80) REVERT: B 190 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: B 380 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7933 (tp30) REVERT: D 417 ASP cc_start: 0.7601 (t70) cc_final: 0.7337 (t70) outliers start: 39 outliers final: 24 residues processed: 209 average time/residue: 0.1986 time to fit residues: 63.2433 Evaluate side-chains 201 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 651 LEU Chi-restraints excluded: chain D residue 662 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: 0.3980 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 A 230 HIS ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119093 restraints weight = 17045.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122872 restraints weight = 9743.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125218 restraints weight = 7062.007| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11750 Z= 0.119 Angle : 0.531 7.114 15826 Z= 0.277 Chirality : 0.041 0.175 1712 Planarity : 0.003 0.052 2026 Dihedral : 4.594 36.422 1552 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.15 % Allowed : 22.18 % Favored : 74.68 % 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: -1.79 (0.41), residues: 148 loop : -0.02 (0.25), residues: 692 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 0.023 0.001 PHE C 573 TYR 0.023 0.001 TYR D 422 ARG 0.002 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 473) hydrogen bonds : angle 4.75327 ( 1305) covalent geometry : bond 0.00274 (11750) covalent geometry : angle 0.53079 (15826) *********************** 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 215 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.264 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: 0.7876 (mp10) REVERT: A 265 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 370 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8371 (m) REVERT: C 431 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8587 (pp) REVERT: C 445 TRP cc_start: 0.6681 (OUTLIER) cc_final: 0.5813 (m100) REVERT: C 517 MET cc_start: 0.2072 (ppp) cc_final: -0.0031 (ptt) REVERT: C 583 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7869 (tp40) REVERT: C 659 PHE cc_start: 0.6833 (m-80) cc_final: 0.6443 (m-80) REVERT: B 190 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: B 265 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 380 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7859 (tp30) REVERT: B 413 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 417 ASP cc_start: 0.7616 (t70) cc_final: 0.7332 (t70) REVERT: D 422 TYR cc_start: 0.8203 (m-80) cc_final: 0.7979 (m-10) outliers start: 39 outliers final: 28 residues processed: 201 average time/residue: 0.1998 time to fit residues: 61.1994 Evaluate side-chains 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 101 GLN 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.0370 chunk 79 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 103 ASN ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114280 restraints weight = 17236.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117920 restraints weight = 9839.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120259 restraints weight = 7179.839| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11750 Z= 0.165 Angle : 0.568 8.372 15826 Z= 0.294 Chirality : 0.042 0.214 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.690 35.494 1552 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % 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: 0.05 (0.23), residues: 1422 helix: 0.77 (0.22), residues: 582 sheet: -1.87 (0.41), residues: 150 loop : -0.00 (0.25), residues: 690 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 0.021 0.001 TYR D 422 ARG 0.003 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 473) hydrogen bonds : angle 4.80878 ( 1305) covalent geometry : bond 0.00389 (11750) covalent geometry : angle 0.56797 (15826) *********************** 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 222 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8148 (mp10) cc_final: 0.7790 (mp10) REVERT: A 17 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.6722 (mt) REVERT: A 265 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7085 (tm-30) REVERT: C 431 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8618 (pp) REVERT: C 445 TRP cc_start: 0.6828 (OUTLIER) cc_final: 0.5959 (m100) REVERT: C 517 MET cc_start: 0.1968 (ppp) cc_final: -0.0301 (ptt) REVERT: C 583 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7898 (tp40) REVERT: C 605 PHE cc_start: 0.8819 (m-10) cc_final: 0.8616 (m-10) REVERT: C 659 PHE cc_start: 0.6880 (m-80) cc_final: 0.6488 (m-80) REVERT: B 190 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: B 265 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 300 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7581 (mtm-85) REVERT: B 380 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7915 (tp30) REVERT: B 413 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7860 (mt-10) outliers start: 44 outliers final: 33 residues processed: 207 average time/residue: 0.2147 time to fit residues: 66.3266 Evaluate side-chains 208 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 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 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 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 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 D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 629 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116451 restraints weight = 17116.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120195 restraints weight = 9691.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122419 restraints weight = 7013.988| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11750 Z= 0.123 Angle : 0.548 7.860 15826 Z= 0.283 Chirality : 0.042 0.209 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.671 34.091 1552 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.31 % Allowed : 22.58 % Favored : 74.11 % 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: 0.15 (0.23), residues: 1422 helix: 0.83 (0.22), residues: 580 sheet: -1.85 (0.42), residues: 150 loop : 0.07 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 655 HIS 0.004 0.001 HIS B 288 PHE 0.021 0.001 PHE B 350 TYR 0.023 0.001 TYR D 422 ARG 0.002 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 473) hydrogen bonds : angle 4.73189 ( 1305) covalent geometry : bond 0.00287 (11750) covalent geometry : angle 0.54750 (15826) *********************** 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 221 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8075 (mp10) cc_final: 0.7515 (mp10) REVERT: A 17 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.6711 (mt) REVERT: A 265 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7052 (tm-30) REVERT: C 431 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8602 (pp) REVERT: C 517 MET cc_start: 0.1880 (ppp) cc_final: -0.0316 (ptt) REVERT: C 583 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7814 (tp40) REVERT: C 605 PHE cc_start: 0.8740 (m-10) cc_final: 0.8519 (m-10) REVERT: C 655 TRP cc_start: 0.8422 (p-90) cc_final: 0.8170 (p-90) REVERT: B 190 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: B 265 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 300 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7542 (mtm-85) REVERT: B 380 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7909 (tp30) REVERT: B 413 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7824 (mt-10) outliers start: 41 outliers final: 32 residues processed: 204 average time/residue: 0.2068 time to fit residues: 63.4767 Evaluate side-chains 207 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 101 GLN 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 A residue 360 ILE 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 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 195 THR 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 300 ARG 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 629 LEU 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: 7.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 103 ASN ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN D 654 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114343 restraints weight = 17262.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118002 restraints weight = 9909.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120344 restraints weight = 7249.134| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2280 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= 0.166 Angle : 0.588 9.083 15826 Z= 0.302 Chirality : 0.042 0.223 1712 Planarity : 0.003 0.055 2026 Dihedral : 4.757 36.942 1552 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.23 % Allowed : 23.39 % 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: 0.09 (0.23), residues: 1422 helix: 0.82 (0.22), residues: 580 sheet: -1.84 (0.42), residues: 150 loop : 0.00 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 655 HIS 0.004 0.001 HIS B 288 PHE 0.024 0.002 PHE A 350 TYR 0.032 0.001 TYR D 422 ARG 0.005 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 473) hydrogen bonds : angle 4.75450 ( 1305) covalent geometry : bond 0.00391 (11750) covalent geometry : angle 0.58845 (15826) *********************** 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 213 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8127 (mp10) cc_final: 0.7533 (mp10) REVERT: A 17 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.6690 (mt) REVERT: A 265 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7146 (tm-30) REVERT: C 431 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8640 (pp) REVERT: C 517 MET cc_start: 0.1647 (ppp) cc_final: -0.0407 (ptt) REVERT: C 605 PHE cc_start: 0.8825 (m-10) cc_final: 0.8538 (m-10) REVERT: B 190 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: B 265 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7072 (tm-30) REVERT: B 380 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7954 (tp30) REVERT: B 413 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7857 (mt-10) outliers start: 40 outliers final: 32 residues processed: 199 average time/residue: 0.1977 time to fit residues: 59.4539 Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 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 A residue 360 ILE 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 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 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 629 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117018 restraints weight = 17115.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120819 restraints weight = 9760.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123065 restraints weight = 7108.932| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11750 Z= 0.124 Angle : 0.575 9.023 15826 Z= 0.295 Chirality : 0.042 0.233 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.733 42.990 1552 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.98 % Allowed : 23.55 % Favored : 73.47 % 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: 0.10 (0.23), residues: 1422 helix: 0.82 (0.22), residues: 580 sheet: -1.82 (0.42), residues: 150 loop : 0.01 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 655 HIS 0.003 0.001 HIS B 288 PHE 0.030 0.002 PHE A 359 TYR 0.041 0.001 TYR D 422 ARG 0.008 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 473) hydrogen bonds : angle 4.72687 ( 1305) covalent geometry : bond 0.00289 (11750) covalent geometry : angle 0.57471 (15826) ********************** 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 219 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8045 (mp10) cc_final: 0.7502 (mp10) REVERT: A 9 LYS cc_start: 0.8649 (tppt) cc_final: 0.8402 (tppt) REVERT: A 17 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.6745 (mt) REVERT: A 265 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7113 (tm-30) REVERT: C 431 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8429 (pp) REVERT: C 517 MET cc_start: 0.1856 (ppp) cc_final: -0.0176 (ptt) REVERT: C 605 PHE cc_start: 0.8784 (m-10) cc_final: 0.8527 (m-10) REVERT: B 190 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8180 (mt0) REVERT: B 265 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 300 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7722 (mtm-85) REVERT: B 380 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7899 (tp30) REVERT: B 413 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 417 ASP cc_start: 0.7654 (t70) cc_final: 0.7358 (t70) REVERT: D 517 MET cc_start: 0.3298 (pmm) cc_final: 0.2852 (ppp) outliers start: 37 outliers final: 31 residues processed: 205 average time/residue: 0.2069 time to fit residues: 64.3010 Evaluate side-chains 206 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 A residue 360 ILE 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 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 195 THR 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 300 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 91 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121891 restraints weight = 17012.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122630 restraints weight = 10244.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123481 restraints weight = 7661.054| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11750 Z= 0.111 Angle : 0.566 8.676 15826 Z= 0.292 Chirality : 0.042 0.235 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.703 49.874 1552 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.90 % Allowed : 24.11 % Favored : 72.98 % 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: 0.12 (0.23), residues: 1422 helix: 0.84 (0.22), residues: 582 sheet: -1.75 (0.42), residues: 150 loop : -0.00 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 655 HIS 0.003 0.000 HIS B 288 PHE 0.030 0.001 PHE A 359 TYR 0.035 0.001 TYR D 422 ARG 0.008 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 473) hydrogen bonds : angle 4.66012 ( 1305) covalent geometry : bond 0.00254 (11750) covalent geometry : angle 0.56631 (15826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4884.44 seconds wall clock time: 90 minutes 54.31 seconds (5454.31 seconds total)