Starting phenix.real_space_refine on Wed Feb 14 22:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8x_24928/02_2024/7s8x_24928.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8x_24928/02_2024/7s8x_24928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8x_24928/02_2024/7s8x_24928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8x_24928/02_2024/7s8x_24928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8x_24928/02_2024/7s8x_24928.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8x_24928/02_2024/7s8x_24928.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 50 5.16 5 C 6838 2.51 5 N 1676 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 280": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B GLU 666": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5213 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 33, 'TRANS': 641} Chain breaks: 1 Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5213 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 33, 'TRANS': 641} Chain breaks: 1 Time building chain proxies: 5.77, per 1000 atoms: 0.55 Number of scatterers: 10426 At special positions: 0 Unit cell: (115.867, 107.363, 119.056, 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 50 16.00 O 1862 8.00 N 1676 7.00 C 6838 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 - 3.50 Amino acid : False - 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: 4.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 68.1% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.577A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.648A pdb=" N GLN A 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 49 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.160A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.711A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.522A pdb=" N SER A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 196 removed outlier: 4.698A pdb=" N ARG A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.875A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 230 removed outlier: 4.450A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.651A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.440A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.774A pdb=" N GLU A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.797A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.734A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.918A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.109A pdb=" N GLU A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 578 Processing helix chain 'A' and resid 653 through 671 Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.675A pdb=" N ASN A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.577A pdb=" N LEU B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.648A pdb=" N GLN B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 49 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.160A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 127 removed outlier: 3.711A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.523A pdb=" N SER B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 196 removed outlier: 4.698A pdb=" N ARG B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.874A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 230 removed outlier: 4.450A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 307 removed outlier: 3.651A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.443A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.774A pdb=" N GLU B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 434' Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.797A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.736A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 483 through 505 removed outlier: 3.917A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.109A pdb=" N GLU B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 578 Processing helix chain 'B' and resid 653 through 671 Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.675A pdb=" N ASN B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.561A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.562A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 4.47 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: 3218 1.34 - 1.46: 2255 1.46 - 1.58: 5107 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 10662 Sorted by residual: bond pdb=" N VAL B 18 " pdb=" CA VAL B 18 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.42e+00 bond pdb=" N TYR A 17 " pdb=" CA TYR A 17 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.21e-02 6.83e+03 4.93e+00 bond pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.70e+00 bond pdb=" CA LEU B 448 " pdb=" C LEU B 448 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.72e-02 3.38e+03 2.72e+00 bond pdb=" CA LEU A 448 " pdb=" C LEU A 448 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.72e-02 3.38e+03 2.71e+00 ... (remaining 10657 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.27: 302 106.27 - 113.22: 5878 113.22 - 120.17: 3898 120.17 - 127.12: 4324 127.12 - 134.07: 92 Bond angle restraints: 14494 Sorted by residual: angle pdb=" C PRO B 515 " pdb=" N ASP B 516 " pdb=" CA ASP B 516 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C PRO A 515 " pdb=" N ASP A 516 " pdb=" CA ASP A 516 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N ALA B 138 " pdb=" CA ALA B 138 " pdb=" C ALA B 138 " ideal model delta sigma weight residual 110.80 117.73 -6.93 2.13e+00 2.20e-01 1.06e+01 angle pdb=" N ALA A 138 " pdb=" CA ALA A 138 " pdb=" C ALA A 138 " ideal model delta sigma weight residual 110.80 117.70 -6.90 2.13e+00 2.20e-01 1.05e+01 angle pdb=" CA VAL B 18 " pdb=" C VAL B 18 " pdb=" O VAL B 18 " ideal model delta sigma weight residual 120.78 117.19 3.59 1.25e+00 6.40e-01 8.25e+00 ... (remaining 14489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5712 17.78 - 35.55: 500 35.55 - 53.33: 70 53.33 - 71.11: 16 71.11 - 88.89: 14 Dihedral angle restraints: 6312 sinusoidal: 2418 harmonic: 3894 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PHE B 76 " pdb=" C PHE B 76 " pdb=" N LYS B 77 " pdb=" CA LYS B 77 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1140 0.041 - 0.083: 435 0.083 - 0.124: 126 0.124 - 0.165: 19 0.165 - 0.206: 2 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CB THR A 390 " pdb=" CA THR A 390 " pdb=" OG1 THR A 390 " pdb=" CG2 THR A 390 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR B 390 " pdb=" CA THR B 390 " pdb=" OG1 THR B 390 " pdb=" CG2 THR B 390 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ASP B 516 " pdb=" N ASP B 516 " pdb=" C ASP B 516 " pdb=" CB ASP B 516 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1719 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 135 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 136 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 135 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 136 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 286 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 287 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.023 5.00e-02 4.00e+02 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2094 2.77 - 3.30: 10857 3.30 - 3.83: 17417 3.83 - 4.37: 20218 4.37 - 4.90: 34690 Nonbonded interactions: 85276 Sorted by model distance: nonbonded pdb=" OH TYR A 123 " pdb=" OE1 GLU A 374 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR B 123 " pdb=" OE1 GLU B 374 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR A 128 " pdb=" OE2 GLU A 374 " model vdw 2.264 2.440 ... (remaining 85271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.000 Extract box with map and model: 4.110 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.480 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.005 0.047 10662 Z= 0.332 Angle : 0.726 8.441 14494 Z= 0.401 Chirality : 0.046 0.206 1722 Planarity : 0.005 0.042 1806 Dihedral : 14.048 88.885 3820 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.01 (0.23), residues: 1342 helix: 0.88 (0.18), residues: 874 sheet: 1.17 (0.87), residues: 36 loop : -1.89 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 472 HIS 0.003 0.001 HIS A 131 PHE 0.028 0.002 PHE B 111 TYR 0.016 0.002 TYR B 545 ARG 0.010 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.220 Fit side-chains REVERT: A 334 SER cc_start: 0.8071 (p) cc_final: 0.7689 (p) REVERT: A 453 MET cc_start: 0.8131 (mmp) cc_final: 0.7873 (mmm) REVERT: B 180 MET cc_start: 0.6892 (mmm) cc_final: 0.6653 (mmp) REVERT: B 453 MET cc_start: 0.8100 (mmp) cc_final: 0.7894 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1939 time to fit residues: 44.8164 Evaluate side-chains 121 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.0000 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10662 Z= 0.200 Angle : 0.586 6.408 14494 Z= 0.305 Chirality : 0.043 0.154 1722 Planarity : 0.005 0.041 1806 Dihedral : 4.625 19.842 1444 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 0.70 % Allowed : 6.11 % Favored : 93.19 % 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: 0.60 (0.23), residues: 1342 helix: 1.42 (0.18), residues: 862 sheet: 1.12 (0.88), residues: 36 loop : -1.77 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS B 131 PHE 0.024 0.001 PHE A 278 TYR 0.010 0.001 TYR B 367 ARG 0.004 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.188 Fit side-chains REVERT: A 180 MET cc_start: 0.6797 (mmp) cc_final: 0.6481 (mmm) REVERT: A 453 MET cc_start: 0.8080 (mmp) cc_final: 0.7777 (mmm) REVERT: A 548 ASN cc_start: 0.8714 (t0) cc_final: 0.8156 (t0) REVERT: B 453 MET cc_start: 0.8096 (mmp) cc_final: 0.7841 (mmm) REVERT: B 548 ASN cc_start: 0.8611 (t0) cc_final: 0.8213 (t0) outliers start: 8 outliers final: 7 residues processed: 141 average time/residue: 0.1908 time to fit residues: 40.4510 Evaluate side-chains 131 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 0.0570 chunk 120 optimal weight: 0.4980 chunk 41 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10662 Z= 0.179 Angle : 0.542 6.610 14494 Z= 0.283 Chirality : 0.042 0.152 1722 Planarity : 0.004 0.043 1806 Dihedral : 4.397 20.205 1444 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.96 % Rotamer: Outliers : 1.48 % Allowed : 8.46 % Favored : 90.05 % 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: 0.83 (0.23), residues: 1342 helix: 1.59 (0.18), residues: 866 sheet: 1.10 (0.86), residues: 36 loop : -1.66 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.002 0.000 HIS A 131 PHE 0.021 0.001 PHE A 278 TYR 0.009 0.001 TYR A 545 ARG 0.004 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.073 Fit side-chains REVERT: A 548 ASN cc_start: 0.8594 (t0) cc_final: 0.8191 (t0) REVERT: B 548 ASN cc_start: 0.8503 (t0) cc_final: 0.8069 (t0) outliers start: 17 outliers final: 12 residues processed: 141 average time/residue: 0.1905 time to fit residues: 40.2780 Evaluate side-chains 136 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.004 0.049 10662 Z= 0.242 Angle : 0.562 6.679 14494 Z= 0.292 Chirality : 0.043 0.155 1722 Planarity : 0.004 0.043 1806 Dihedral : 4.382 19.805 1444 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.04 % Favored : 93.82 % Rotamer: Outliers : 1.48 % Allowed : 10.91 % Favored : 87.61 % 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: 0.90 (0.23), residues: 1342 helix: 1.66 (0.18), residues: 864 sheet: 1.25 (0.87), residues: 36 loop : -1.68 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS B 131 PHE 0.022 0.001 PHE A 278 TYR 0.011 0.001 TYR B 545 ARG 0.004 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.266 Fit side-chains REVERT: A 548 ASN cc_start: 0.8800 (t0) cc_final: 0.8406 (t0) REVERT: B 180 MET cc_start: 0.7150 (mmm) cc_final: 0.6868 (mmp) REVERT: B 548 ASN cc_start: 0.8717 (t0) cc_final: 0.8300 (t0) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.1821 time to fit residues: 38.4007 Evaluate side-chains 140 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10662 Z= 0.200 Angle : 0.536 6.739 14494 Z= 0.279 Chirality : 0.042 0.145 1722 Planarity : 0.004 0.044 1806 Dihedral : 4.305 20.039 1444 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.04 % Favored : 93.82 % Rotamer: Outliers : 2.01 % Allowed : 11.69 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1342 helix: 1.78 (0.18), residues: 862 sheet: 1.28 (0.86), residues: 36 loop : -1.68 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 472 HIS 0.002 0.000 HIS B 131 PHE 0.020 0.001 PHE A 278 TYR 0.009 0.001 TYR B 545 ARG 0.004 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.238 Fit side-chains REVERT: A 453 MET cc_start: 0.8084 (mmp) cc_final: 0.7757 (mmp) REVERT: A 548 ASN cc_start: 0.8704 (t0) cc_final: 0.8267 (t0) REVERT: B 548 ASN cc_start: 0.8643 (t0) cc_final: 0.8217 (t0) REVERT: B 670 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8623 (t) outliers start: 23 outliers final: 15 residues processed: 143 average time/residue: 0.1848 time to fit residues: 39.9630 Evaluate side-chains 145 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 670 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10662 Z= 0.198 Angle : 0.534 6.677 14494 Z= 0.277 Chirality : 0.042 0.157 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.254 20.020 1444 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 2.62 % Allowed : 11.69 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1342 helix: 1.77 (0.18), residues: 866 sheet: 1.47 (0.86), residues: 36 loop : -1.62 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.002 0.000 HIS B 131 PHE 0.017 0.001 PHE A 278 TYR 0.010 0.001 TYR A 367 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.440 Fit side-chains REVERT: A 453 MET cc_start: 0.8118 (mmp) cc_final: 0.7757 (mmp) REVERT: A 548 ASN cc_start: 0.8689 (t0) cc_final: 0.8239 (t0) REVERT: A 652 MET cc_start: 0.9116 (mtp) cc_final: 0.8830 (mtm) REVERT: B 180 MET cc_start: 0.6976 (mmp) cc_final: 0.6656 (mmm) REVERT: B 548 ASN cc_start: 0.8643 (t0) cc_final: 0.8212 (t0) REVERT: B 670 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8591 (t) outliers start: 30 outliers final: 16 residues processed: 153 average time/residue: 0.1956 time to fit residues: 45.8777 Evaluate side-chains 146 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 670 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 0.0570 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10662 Z= 0.216 Angle : 0.536 6.837 14494 Z= 0.278 Chirality : 0.042 0.156 1722 Planarity : 0.004 0.046 1806 Dihedral : 4.264 19.843 1444 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 2.71 % Allowed : 12.74 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1342 helix: 1.77 (0.18), residues: 868 sheet: 1.54 (0.85), residues: 36 loop : -1.63 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.002 0.000 HIS A 131 PHE 0.016 0.001 PHE A 278 TYR 0.009 0.001 TYR A 545 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.231 Fit side-chains REVERT: A 20 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8308 (ptt90) REVERT: A 548 ASN cc_start: 0.8724 (t0) cc_final: 0.8274 (t0) REVERT: A 652 MET cc_start: 0.9111 (mtp) cc_final: 0.8820 (mtm) REVERT: B 180 MET cc_start: 0.7091 (mmp) cc_final: 0.6776 (mmm) REVERT: B 548 ASN cc_start: 0.8673 (t0) cc_final: 0.8238 (t0) outliers start: 31 outliers final: 19 residues processed: 150 average time/residue: 0.1825 time to fit residues: 41.7214 Evaluate side-chains 147 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 670 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10662 Z= 0.206 Angle : 0.531 7.064 14494 Z= 0.276 Chirality : 0.042 0.154 1722 Planarity : 0.004 0.047 1806 Dihedral : 4.238 19.859 1444 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 2.27 % Allowed : 13.26 % Favored : 84.47 % 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: 1.10 (0.24), residues: 1342 helix: 1.80 (0.18), residues: 868 sheet: 1.57 (0.85), residues: 36 loop : -1.60 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 472 HIS 0.002 0.000 HIS B 131 PHE 0.015 0.001 PHE A 278 TYR 0.009 0.001 TYR B 367 ARG 0.003 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.237 Fit side-chains REVERT: A 20 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8319 (ptt90) REVERT: A 548 ASN cc_start: 0.8700 (t0) cc_final: 0.8246 (t0) REVERT: A 652 MET cc_start: 0.9094 (mtp) cc_final: 0.8887 (mtm) REVERT: B 180 MET cc_start: 0.7143 (mmp) cc_final: 0.6790 (mmm) REVERT: B 357 MET cc_start: 0.8501 (tpp) cc_final: 0.8279 (tpt) REVERT: B 548 ASN cc_start: 0.8665 (t0) cc_final: 0.8227 (t0) outliers start: 26 outliers final: 21 residues processed: 146 average time/residue: 0.1824 time to fit residues: 40.9153 Evaluate side-chains 149 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 670 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10662 Z= 0.232 Angle : 0.553 12.119 14494 Z= 0.285 Chirality : 0.043 0.157 1722 Planarity : 0.004 0.047 1806 Dihedral : 4.274 19.605 1444 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 2.53 % Allowed : 13.18 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1342 helix: 1.76 (0.18), residues: 868 sheet: 1.58 (0.86), residues: 36 loop : -1.62 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.002 0.001 HIS A 131 PHE 0.016 0.001 PHE B 111 TYR 0.009 0.001 TYR A 546 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.211 Fit side-chains REVERT: A 20 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (ptt90) REVERT: A 548 ASN cc_start: 0.8738 (t0) cc_final: 0.8293 (t0) REVERT: B 180 MET cc_start: 0.7042 (mmp) cc_final: 0.6721 (mmm) REVERT: B 548 ASN cc_start: 0.8712 (t0) cc_final: 0.8277 (t0) outliers start: 29 outliers final: 24 residues processed: 149 average time/residue: 0.1837 time to fit residues: 42.0601 Evaluate side-chains 152 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10662 Z= 0.194 Angle : 0.544 12.920 14494 Z= 0.278 Chirality : 0.042 0.156 1722 Planarity : 0.004 0.048 1806 Dihedral : 4.257 20.005 1444 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.96 % Rotamer: Outliers : 2.18 % Allowed : 13.87 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1342 helix: 1.81 (0.18), residues: 868 sheet: 1.56 (0.85), residues: 36 loop : -1.60 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.002 0.000 HIS B 131 PHE 0.015 0.001 PHE A 278 TYR 0.034 0.001 TYR A 526 ARG 0.003 0.000 ARG B 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.140 Fit side-chains REVERT: A 20 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (ptt90) REVERT: A 548 ASN cc_start: 0.8658 (t0) cc_final: 0.8219 (t0) REVERT: B 20 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8317 (tmm160) REVERT: B 180 MET cc_start: 0.6969 (mmp) cc_final: 0.6728 (mmm) REVERT: B 299 MET cc_start: 0.7488 (mmt) cc_final: 0.7272 (mmm) REVERT: B 548 ASN cc_start: 0.8633 (t0) cc_final: 0.8196 (t0) outliers start: 25 outliers final: 22 residues processed: 147 average time/residue: 0.1927 time to fit residues: 41.9992 Evaluate side-chains 150 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115180 restraints weight = 13110.224| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.65 r_work: 0.2903 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10662 Z= 0.210 Angle : 0.547 12.937 14494 Z= 0.280 Chirality : 0.042 0.157 1722 Planarity : 0.004 0.048 1806 Dihedral : 4.257 19.878 1444 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 2.88 % Allowed : 13.61 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1342 helix: 1.79 (0.18), residues: 868 sheet: 1.55 (0.86), residues: 36 loop : -1.57 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.002 0.001 HIS B 131 PHE 0.015 0.001 PHE A 111 TYR 0.026 0.001 TYR A 526 ARG 0.003 0.000 ARG B 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.30 seconds wall clock time: 38 minutes 28.24 seconds (2308.24 seconds total)