Starting phenix.real_space_refine on Sat Oct 12 04:24:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo3_39434/10_2024/8yo3_39434.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo3_39434/10_2024/8yo3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo3_39434/10_2024/8yo3_39434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo3_39434/10_2024/8yo3_39434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo3_39434/10_2024/8yo3_39434.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo3_39434/10_2024/8yo3_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-5477/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: 7.09, per 1000 atoms: 0.62 Number of scatterers: 11514 At special positions: 0 Unit cell: (108, 147, 113, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2164 8.00 N 1948 7.00 C 7360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 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: 1.44 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: 4.20 Time building geometry restraints manager: 3.12 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.650 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11750 Z= 0.157 Angle : 0.570 12.152 15826 Z= 0.298 Chirality : 0.040 0.199 1712 Planarity : 0.003 0.035 2026 Dihedral : 16.911 89.260 4420 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.73 % Allowed : 24.11 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1422 helix: 0.54 (0.23), residues: 564 sheet: -0.61 (0.41), residues: 190 loop : -0.04 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 655 HIS 0.008 0.001 HIS B 358 PHE 0.031 0.001 PHE B 359 TYR 0.016 0.001 TYR C 422 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.343 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: 0.2049 time to fit residues: 55.5075 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11750 Z= 0.196 Angle : 0.554 7.674 15826 Z= 0.295 Chirality : 0.042 0.164 1712 Planarity : 0.003 0.044 2026 Dihedral : 5.137 57.310 1560 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.74 % Allowed : 21.77 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1422 helix: 0.52 (0.22), residues: 582 sheet: -1.21 (0.39), residues: 170 loop : -0.03 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 655 HIS 0.006 0.001 HIS B 288 PHE 0.025 0.001 PHE B 350 TYR 0.016 0.001 TYR C 422 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 431 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8118 (pp) REVERT: C 517 MET cc_start: 0.0200 (ppp) cc_final: -0.0624 (pmm) REVERT: B 380 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7663 (tp30) REVERT: D 417 ASP cc_start: 0.7541 (t70) cc_final: 0.7299 (t70) outliers start: 34 outliers final: 17 residues processed: 207 average time/residue: 0.2239 time to fit residues: 69.9580 Evaluate side-chains 182 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 71 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11750 Z= 0.332 Angle : 0.584 7.769 15826 Z= 0.308 Chirality : 0.043 0.168 1712 Planarity : 0.004 0.051 2026 Dihedral : 4.861 36.465 1552 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.39 % Allowed : 20.73 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1422 helix: 0.57 (0.22), residues: 580 sheet: -1.95 (0.41), residues: 148 loop : -0.10 (0.25), residues: 694 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 0.020 0.002 PHE B 350 TYR 0.021 0.002 TYR C 422 ARG 0.005 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.6466 (mt) REVERT: A 265 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7096 (tm-30) REVERT: C 431 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 447 MET cc_start: 0.4950 (tmm) cc_final: 0.4600 (tmm) REVERT: C 547 MET cc_start: 0.8268 (mmm) cc_final: 0.7984 (mtt) REVERT: B 190 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: B 380 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7713 (tp30) REVERT: D 422 TYR cc_start: 0.8321 (m-80) cc_final: 0.8109 (m-10) outliers start: 42 outliers final: 27 residues processed: 204 average time/residue: 0.2152 time to fit residues: 66.6421 Evaluate side-chains 194 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 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 566 ILE Chi-restraints excluded: chain D residue 595 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 127 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 129 optimal weight: 0.0980 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN C 497 ASN ** D 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11750 Z= 0.156 Angle : 0.514 7.172 15826 Z= 0.271 Chirality : 0.041 0.173 1712 Planarity : 0.003 0.049 2026 Dihedral : 4.696 36.096 1552 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.39 % Allowed : 21.29 % Favored : 75.32 % 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: -0.01 (0.23), residues: 1422 helix: 0.66 (0.22), residues: 582 sheet: -1.97 (0.41), residues: 150 loop : 0.04 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 655 HIS 0.010 0.001 HIS D 397 PHE 0.018 0.001 PHE D 605 TYR 0.013 0.001 TYR C 422 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8315 (mp10) cc_final: 0.8080 (mp10) REVERT: A 265 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 431 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8412 (pp) REVERT: C 447 MET cc_start: 0.4501 (tmm) cc_final: 0.4283 (tmm) REVERT: C 517 MET cc_start: 0.1117 (ppp) cc_final: -0.0867 (ptt) REVERT: B 190 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: B 380 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7664 (tp30) REVERT: D 417 ASP cc_start: 0.7557 (t70) cc_final: 0.7309 (t70) outliers start: 42 outliers final: 23 residues processed: 211 average time/residue: 0.2245 time to fit residues: 72.3717 Evaluate side-chains 192 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 318 ASP 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 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 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11750 Z= 0.326 Angle : 0.590 8.889 15826 Z= 0.305 Chirality : 0.043 0.182 1712 Planarity : 0.004 0.054 2026 Dihedral : 4.833 36.250 1552 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.55 % Allowed : 21.45 % 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: -0.05 (0.23), residues: 1422 helix: 0.65 (0.22), residues: 582 sheet: -2.01 (0.41), residues: 150 loop : -0.01 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 655 HIS 0.010 0.001 HIS D 397 PHE 0.022 0.002 PHE B 350 TYR 0.022 0.002 TYR C 435 ARG 0.005 0.000 ARG A 6 *********************** 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 225 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.6560 (mt) REVERT: A 265 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7088 (tm-30) REVERT: C 431 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8535 (pp) REVERT: C 517 MET cc_start: 0.1217 (ppp) cc_final: -0.0818 (ptt) REVERT: B 190 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: B 265 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 380 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7724 (tp30) outliers start: 44 outliers final: 29 residues processed: 210 average time/residue: 0.2031 time to fit residues: 65.0173 Evaluate side-chains 203 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU 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 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 386 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 45 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11750 Z= 0.162 Angle : 0.532 7.786 15826 Z= 0.278 Chirality : 0.041 0.185 1712 Planarity : 0.003 0.053 2026 Dihedral : 4.729 34.478 1552 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.06 % Allowed : 23.06 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1422 helix: 0.70 (0.22), residues: 580 sheet: -1.98 (0.41), residues: 150 loop : 0.02 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 655 HIS 0.006 0.001 HIS C 397 PHE 0.028 0.002 PHE C 573 TYR 0.015 0.001 TYR C 435 ARG 0.007 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6545 (mt) REVERT: A 265 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6988 (tm-30) REVERT: C 422 TYR cc_start: 0.8089 (m-80) cc_final: 0.7868 (m-10) REVERT: C 431 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8541 (pp) REVERT: C 517 MET cc_start: 0.1008 (ppp) cc_final: -0.1021 (ptt) REVERT: B 190 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: B 265 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 380 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7683 (tp30) REVERT: B 413 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 417 ASP cc_start: 0.7524 (t70) cc_final: 0.7296 (t70) outliers start: 38 outliers final: 27 residues processed: 209 average time/residue: 0.2046 time to fit residues: 65.0633 Evaluate side-chains 202 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain 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 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 663 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 136 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.0770 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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** D 432 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2089 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= 0.154 Angle : 0.545 7.776 15826 Z= 0.282 Chirality : 0.041 0.194 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.642 33.909 1552 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.39 % Allowed : 22.34 % Favored : 74.27 % 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 (0.24), residues: 1422 helix: 0.72 (0.22), residues: 592 sheet: -1.84 (0.42), residues: 150 loop : 0.08 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 655 HIS 0.004 0.001 HIS D 397 PHE 0.018 0.001 PHE D 605 TYR 0.028 0.001 TYR D 422 ARG 0.007 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6547 (mt) REVERT: A 265 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 431 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8424 (pp) REVERT: C 627 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8144 (mtmm) REVERT: B 190 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: B 265 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6991 (tm-30) REVERT: B 380 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7664 (tp30) REVERT: B 413 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7562 (mt-10) REVERT: D 417 ASP cc_start: 0.7536 (t70) cc_final: 0.7300 (t70) outliers start: 42 outliers final: 29 residues processed: 214 average time/residue: 0.2131 time to fit residues: 68.1197 Evaluate side-chains 209 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 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 627 LYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 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 556 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 54 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 131 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN D 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11750 Z= 0.488 Angle : 0.706 11.641 15826 Z= 0.363 Chirality : 0.046 0.253 1712 Planarity : 0.004 0.061 2026 Dihedral : 5.069 34.618 1552 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.39 % Allowed : 23.15 % 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: -0.12 (0.23), residues: 1422 helix: 0.64 (0.22), residues: 578 sheet: -2.01 (0.41), residues: 150 loop : -0.10 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 655 HIS 0.009 0.001 HIS D 397 PHE 0.030 0.002 PHE A 359 TYR 0.026 0.002 TYR C 422 ARG 0.005 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 431 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8566 (pp) REVERT: C 445 TRP cc_start: 0.6882 (OUTLIER) cc_final: 0.5987 (m100) REVERT: C 627 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7793 (mttp) REVERT: B 190 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: B 265 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 380 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7797 (tp30) outliers start: 42 outliers final: 33 residues processed: 200 average time/residue: 0.2116 time to fit residues: 62.8980 Evaluate side-chains 204 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 445 TRP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 627 LYS 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 138 VAL 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 566 ILE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 651 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 119 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 0.0030 chunk 115 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 83 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11750 Z= 0.181 Angle : 0.586 8.509 15826 Z= 0.301 Chirality : 0.042 0.230 1712 Planarity : 0.003 0.056 2026 Dihedral : 4.919 40.874 1552 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.82 % Allowed : 24.19 % 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: -0.05 (0.23), residues: 1422 helix: 0.64 (0.22), residues: 582 sheet: -1.95 (0.42), residues: 150 loop : -0.01 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 655 HIS 0.005 0.001 HIS D 397 PHE 0.030 0.002 PHE A 359 TYR 0.028 0.001 TYR C 435 ARG 0.008 0.000 ARG A 52 *********************** 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 208 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.6668 (mt) REVERT: A 265 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 431 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8488 (pp) REVERT: C 445 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5816 (m100) REVERT: C 655 TRP cc_start: 0.8384 (p-90) cc_final: 0.8164 (p-90) REVERT: C 659 PHE cc_start: 0.6690 (m-80) cc_final: 0.6386 (m-80) REVERT: B 190 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: B 265 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7040 (tm-30) REVERT: B 380 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7718 (tp30) outliers start: 35 outliers final: 28 residues processed: 193 average time/residue: 0.2110 time to fit residues: 62.1294 Evaluate side-chains 198 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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 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 445 TRP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 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 410 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11750 Z= 0.304 Angle : 0.625 9.431 15826 Z= 0.321 Chirality : 0.043 0.241 1712 Planarity : 0.004 0.056 2026 Dihedral : 4.976 46.707 1552 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.82 % Allowed : 24.44 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1422 helix: 0.63 (0.22), residues: 582 sheet: -1.98 (0.41), residues: 150 loop : -0.03 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 655 HIS 0.007 0.001 HIS D 397 PHE 0.034 0.002 PHE A 359 TYR 0.026 0.002 TYR C 435 ARG 0.007 0.001 ARG A 6 ********************** 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 204 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 445 TRP cc_start: 0.6742 (OUTLIER) cc_final: 0.5789 (m100) REVERT: C 549 TYR cc_start: 0.8518 (m-80) cc_final: 0.8053 (m-80) REVERT: C 604 TRP cc_start: 0.8939 (m-10) cc_final: 0.8713 (m-10) REVERT: B 190 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: B 265 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7093 (tm-30) REVERT: B 380 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7727 (tp30) outliers start: 35 outliers final: 31 residues processed: 191 average time/residue: 0.1982 time to fit residues: 57.7934 Evaluate side-chains 199 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 138 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 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 445 TRP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 557 ASP 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 663 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 0.0470 chunk 20 optimal weight: 0.0370 chunk 99 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.168510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124081 restraints weight = 17010.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123672 restraints weight = 9158.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123861 restraints weight = 8606.847| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11750 Z= 0.175 Angle : 0.589 9.398 15826 Z= 0.301 Chirality : 0.042 0.236 1712 Planarity : 0.003 0.054 2026 Dihedral : 4.921 54.790 1552 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.90 % Allowed : 24.35 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1422 helix: 0.68 (0.22), residues: 582 sheet: -1.49 (0.41), residues: 160 loop : -0.06 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 655 HIS 0.005 0.001 HIS D 397 PHE 0.024 0.002 PHE A 359 TYR 0.024 0.001 TYR C 435 ARG 0.007 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.13 seconds wall clock time: 45 minutes 50.02 seconds (2750.02 seconds total)