Starting phenix.real_space_refine on Mon Mar 11 00:32:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/03_2024/6wu0_21901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/03_2024/6wu0_21901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/03_2024/6wu0_21901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/03_2024/6wu0_21901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/03_2024/6wu0_21901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu0_21901/03_2024/6wu0_21901.pdb" } resolution = 3.59 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 ------------------------------------------------------------------------------- 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= 0.648 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 20 5.16 5 C 4090 2.51 5 N 1097 2.21 5 O 1133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 660": "OD1" <-> "OD2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 718": "NH1" <-> "NH2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 744": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6340 Classifications: {'peptide': 854} Link IDs: {'PTRANS': 52, 'TRANS': 801} Chain breaks: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.63 Number of scatterers: 6340 At special positions: 0 Unit cell: (89.64, 70.2, 131.76, 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 20 16.00 O 1133 8.00 N 1097 7.00 C 4090 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 1 sheets defined 74.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 1 through 15 Processing helix chain 'B' and resid 18 through 38 Processing helix chain 'B' and resid 52 through 66 removed outlier: 3.538A pdb=" N LEU B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 removed outlier: 3.711A pdb=" N ASN B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 70' Processing helix chain 'B' and resid 81 through 102 removed outlier: 4.036A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 126 through 140 Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 152 through 171 removed outlier: 4.107A pdb=" N VAL B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) Proline residue: B 167 - end of helix removed outlier: 3.682A pdb=" N GLY B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 178 through 194 Processing helix chain 'B' and resid 233 through 247 removed outlier: 4.156A pdb=" N ARG B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.713A pdb=" N GLY B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.543A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 333 through 342 removed outlier: 4.315A pdb=" N VAL B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 4.239A pdb=" N ALA B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 397 through 429 removed outlier: 3.500A pdb=" N SER B 401 " --> pdb=" O TYR B 397 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.805A pdb=" N TYR B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.721A pdb=" N LEU B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.563A pdb=" N LEU B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 473 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.521A pdb=" N HIS B 483 " --> pdb=" O ASN B 480 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 485 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 498 removed outlier: 4.491A pdb=" N LEU B 495 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 528 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.719A pdb=" N LYS B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 599 through 614 removed outlier: 3.539A pdb=" N ALA B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 644 removed outlier: 3.538A pdb=" N GLU B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) Proline residue: B 631 - end of helix removed outlier: 3.831A pdb=" N GLN B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 Processing helix chain 'B' and resid 654 through 662 removed outlier: 3.511A pdb=" N VAL B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.671A pdb=" N LEU B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 Processing helix chain 'B' and resid 709 through 739 removed outlier: 3.586A pdb=" N ALA B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 767 removed outlier: 4.126A pdb=" N VAL B 745 " --> pdb=" O ARG B 741 " (cutoff:3.500A) Proline residue: B 751 - end of helix Processing helix chain 'B' and resid 776 through 796 removed outlier: 3.887A pdb=" N MET B 794 " --> pdb=" O VAL B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 799 No H-bonds generated for 'chain 'B' and resid 797 through 799' Processing helix chain 'B' and resid 809 through 828 Processing helix chain 'B' and resid 831 through 854 removed outlier: 4.311A pdb=" N MET B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 850 " --> pdb=" O SER B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 Processing sheet with id=AA1, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.715A pdb=" N ALA B 215 " --> pdb=" O ALA B 79 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1272 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: 1.87 Time building geometry restraints manager: 2.84 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: 2079 1.34 - 1.46: 748 1.46 - 1.57: 3601 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6466 Sorted by residual: bond pdb=" C VAL B 858 " pdb=" O VAL B 858 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.19e-02 7.06e+03 1.05e+00 bond pdb=" CA VAL B 670 " pdb=" CB VAL B 670 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.26e-02 6.30e+03 8.78e-01 bond pdb=" CA VAL B 858 " pdb=" C VAL B 858 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.27e-02 6.20e+03 6.54e-01 bond pdb=" C GLU B 213 " pdb=" N PRO B 214 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.68e-01 bond pdb=" C THR B 260 " pdb=" N GLY B 261 " ideal model delta sigma weight residual 1.331 1.320 0.011 1.46e-02 4.69e+03 5.56e-01 ... (remaining 6461 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.93: 247 106.93 - 113.72: 3755 113.72 - 120.51: 2631 120.51 - 127.31: 2123 127.31 - 134.10: 74 Bond angle restraints: 8830 Sorted by residual: angle pdb=" C ASP B 665 " pdb=" N GLY B 666 " pdb=" CA GLY B 666 " ideal model delta sigma weight residual 121.41 127.46 -6.05 1.96e+00 2.60e-01 9.51e+00 angle pdb=" C VAL B 750 " pdb=" CA VAL B 750 " pdb=" CB VAL B 750 " ideal model delta sigma weight residual 113.70 110.92 2.78 9.50e-01 1.11e+00 8.54e+00 angle pdb=" C LEU B 749 " pdb=" N VAL B 750 " pdb=" CA VAL B 750 " ideal model delta sigma weight residual 120.43 123.12 -2.69 9.60e-01 1.09e+00 7.83e+00 angle pdb=" CA LEU B 498 " pdb=" CB LEU B 498 " pdb=" CG LEU B 498 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" N ARG B 740 " pdb=" CA ARG B 740 " pdb=" C ARG B 740 " ideal model delta sigma weight residual 110.80 115.94 -5.14 2.13e+00 2.20e-01 5.83e+00 ... (remaining 8825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 3480 16.09 - 32.18: 328 32.18 - 48.27: 80 48.27 - 64.36: 13 64.36 - 80.45: 3 Dihedral angle restraints: 3904 sinusoidal: 1447 harmonic: 2457 Sorted by residual: dihedral pdb=" CA GLY B 666 " pdb=" C GLY B 666 " pdb=" N ARG B 667 " pdb=" CA ARG B 667 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ARG B 667 " pdb=" C ARG B 667 " pdb=" N ALA B 668 " pdb=" CA ALA B 668 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 739 " pdb=" C LEU B 739 " pdb=" N ARG B 740 " pdb=" CA ARG B 740 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 836 0.045 - 0.090: 197 0.090 - 0.134: 54 0.134 - 0.179: 0 0.179 - 0.224: 1 Chirality restraints: 1088 Sorted by residual: chirality pdb=" CB ILE B 662 " pdb=" CA ILE B 662 " pdb=" CG1 ILE B 662 " pdb=" CG2 ILE B 662 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 804 " pdb=" CB LEU B 804 " pdb=" CD1 LEU B 804 " pdb=" CD2 LEU B 804 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE B 542 " pdb=" N ILE B 542 " pdb=" C ILE B 542 " pdb=" CB ILE B 542 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1085 not shown) Planarity restraints: 1123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 572 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 573 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 573 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 573 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 440 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO B 441 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 441 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 441 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 513 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO B 514 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " -0.018 5.00e-02 4.00e+02 ... (remaining 1120 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 799 2.75 - 3.29: 6708 3.29 - 3.82: 10517 3.82 - 4.36: 11236 4.36 - 4.90: 19392 Nonbonded interactions: 48652 Sorted by model distance: nonbonded pdb=" O PRO B 167 " pdb=" OG SER B 170 " model vdw 2.211 2.440 nonbonded pdb=" OG SER B 829 " pdb=" OG1 THR B 834 " model vdw 2.256 2.440 nonbonded pdb=" O PHE B 392 " pdb=" OG1 THR B 395 " model vdw 2.261 2.440 nonbonded pdb=" O ARG B 98 " pdb=" NH1 ARG B 98 " model vdw 2.291 2.520 nonbonded pdb=" O PRO B 151 " pdb=" OG SER B 629 " model vdw 2.298 2.440 ... (remaining 48647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.020 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 21.620 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 : 0.003 0.023 6466 Z= 0.170 Angle : 0.647 8.562 8830 Z= 0.342 Chirality : 0.040 0.224 1088 Planarity : 0.004 0.040 1123 Dihedral : 13.427 80.447 2308 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % 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: -1.89 (0.27), residues: 850 helix: -0.45 (0.20), residues: 562 sheet: -1.69 (0.88), residues: 38 loop : -2.89 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 12 HIS 0.002 0.001 HIS B 810 PHE 0.011 0.001 PHE B 270 TYR 0.011 0.001 TYR B 353 ARG 0.002 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6873 (mtt90) REVERT: B 216 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.6619 (mtm-85) REVERT: B 492 MET cc_start: 0.6525 (ptm) cc_final: 0.6195 (ptm) REVERT: B 632 LEU cc_start: 0.8448 (tp) cc_final: 0.8048 (tp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1988 time to fit residues: 39.7552 Evaluate side-chains 124 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 222 GLN B 474 HIS B 483 HIS B 548 GLN B 656 GLN B 722 GLN B 831 HIS B 856 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6466 Z= 0.237 Angle : 0.679 7.704 8830 Z= 0.337 Chirality : 0.043 0.178 1088 Planarity : 0.005 0.067 1123 Dihedral : 4.343 24.909 906 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.05 % Allowed : 15.24 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.29), residues: 850 helix: 0.34 (0.21), residues: 587 sheet: -1.17 (0.92), residues: 38 loop : -3.01 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 827 HIS 0.002 0.001 HIS B 37 PHE 0.021 0.001 PHE B 389 TYR 0.011 0.001 TYR B 353 ARG 0.003 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 492 MET cc_start: 0.6842 (ptm) cc_final: 0.6499 (ptm) REVERT: B 632 LEU cc_start: 0.8519 (tp) cc_final: 0.8171 (tp) REVERT: B 766 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7230 (tt) REVERT: B 794 MET cc_start: 0.5155 (mtp) cc_final: 0.4822 (mtm) REVERT: B 827 TRP cc_start: 0.7405 (t60) cc_final: 0.7179 (t60) REVERT: B 839 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7015 (ptm-80) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.1787 time to fit residues: 32.6865 Evaluate side-chains 133 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 222 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6466 Z= 0.176 Angle : 0.626 7.614 8830 Z= 0.306 Chirality : 0.040 0.158 1088 Planarity : 0.005 0.051 1123 Dihedral : 4.226 23.968 906 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.51 % Allowed : 18.90 % Favored : 77.59 % 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: -0.26 (0.30), residues: 850 helix: 0.88 (0.22), residues: 583 sheet: -0.78 (0.90), residues: 38 loop : -2.83 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 827 HIS 0.002 0.000 HIS B 453 PHE 0.015 0.001 PHE B 720 TYR 0.009 0.001 TYR B 353 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5766 (OUTLIER) cc_final: 0.5222 (t-90) REVERT: B 38 HIS cc_start: 0.6703 (m-70) cc_final: 0.6273 (m-70) REVERT: B 62 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7370 (tt) REVERT: B 118 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6844 (mm-30) REVERT: B 324 VAL cc_start: 0.8056 (p) cc_final: 0.7826 (m) REVERT: B 380 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6212 (tt) REVERT: B 451 ASP cc_start: 0.1995 (OUTLIER) cc_final: -0.1575 (t0) REVERT: B 492 MET cc_start: 0.6781 (ptm) cc_final: 0.6458 (ptm) REVERT: B 632 LEU cc_start: 0.8463 (tp) cc_final: 0.8249 (tt) REVERT: B 766 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7365 (tt) REVERT: B 794 MET cc_start: 0.4976 (mtp) cc_final: 0.4707 (mtm) outliers start: 23 outliers final: 12 residues processed: 139 average time/residue: 0.1723 time to fit residues: 32.1402 Evaluate side-chains 138 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 6466 Z= 0.313 Angle : 0.719 7.889 8830 Z= 0.359 Chirality : 0.043 0.144 1088 Planarity : 0.005 0.050 1123 Dihedral : 4.572 27.648 906 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.71 % Allowed : 19.05 % Favored : 74.24 % 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: -0.39 (0.30), residues: 850 helix: 0.79 (0.22), residues: 580 sheet: -1.09 (0.86), residues: 38 loop : -2.82 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 827 HIS 0.017 0.002 HIS B 37 PHE 0.017 0.001 PHE B 628 TYR 0.015 0.002 TYR B 353 ARG 0.004 0.001 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 LEU cc_start: 0.1622 (OUTLIER) cc_final: 0.1173 (tt) REVERT: B 37 HIS cc_start: 0.5930 (OUTLIER) cc_final: 0.5499 (t70) REVERT: B 38 HIS cc_start: 0.6896 (m-70) cc_final: 0.6347 (m-70) REVERT: B 62 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7626 (tt) REVERT: B 118 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6838 (mm-30) REVERT: B 380 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6377 (tt) REVERT: B 451 ASP cc_start: 0.2251 (OUTLIER) cc_final: -0.1381 (t0) REVERT: B 492 MET cc_start: 0.6934 (ptm) cc_final: 0.6593 (ptm) REVERT: B 632 LEU cc_start: 0.8531 (tp) cc_final: 0.8320 (tt) REVERT: B 766 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7426 (tt) REVERT: B 794 MET cc_start: 0.5118 (mtp) cc_final: 0.4719 (mtm) REVERT: B 827 TRP cc_start: 0.7477 (t60) cc_final: 0.6984 (t-100) REVERT: B 839 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7157 (ptm-80) outliers start: 44 outliers final: 25 residues processed: 149 average time/residue: 0.1705 time to fit residues: 34.1269 Evaluate side-chains 152 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6466 Z= 0.224 Angle : 0.684 7.900 8830 Z= 0.334 Chirality : 0.042 0.174 1088 Planarity : 0.005 0.048 1123 Dihedral : 4.541 26.485 906 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.34 % Allowed : 22.41 % Favored : 72.26 % 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: -0.17 (0.30), residues: 850 helix: 0.91 (0.22), residues: 581 sheet: -0.86 (0.89), residues: 38 loop : -2.63 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 827 HIS 0.003 0.001 HIS B 453 PHE 0.017 0.001 PHE B 720 TYR 0.013 0.001 TYR B 353 ARG 0.004 0.000 ARG B 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 LEU cc_start: 0.1782 (OUTLIER) cc_final: 0.1446 (tt) REVERT: B 37 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5449 (t70) REVERT: B 38 HIS cc_start: 0.6874 (m-70) cc_final: 0.6329 (m-70) REVERT: B 62 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7575 (tt) REVERT: B 380 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6369 (tt) REVERT: B 451 ASP cc_start: 0.2208 (OUTLIER) cc_final: -0.1382 (t0) REVERT: B 459 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 492 MET cc_start: 0.6859 (ptm) cc_final: 0.6547 (ptm) REVERT: B 632 LEU cc_start: 0.8497 (tp) cc_final: 0.8289 (tt) REVERT: B 766 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7341 (tt) REVERT: B 794 MET cc_start: 0.5069 (mtp) cc_final: 0.4695 (mtm) REVERT: B 827 TRP cc_start: 0.7500 (t60) cc_final: 0.7286 (t60) outliers start: 35 outliers final: 22 residues processed: 144 average time/residue: 0.1649 time to fit residues: 32.0263 Evaluate side-chains 150 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6466 Z= 0.207 Angle : 0.691 8.396 8830 Z= 0.333 Chirality : 0.042 0.157 1088 Planarity : 0.005 0.046 1123 Dihedral : 4.485 27.360 906 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.86 % Allowed : 23.02 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.30), residues: 850 helix: 1.15 (0.22), residues: 574 sheet: -0.67 (0.89), residues: 38 loop : -2.63 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 827 HIS 0.002 0.001 HIS B 711 PHE 0.019 0.001 PHE B 720 TYR 0.013 0.001 TYR B 353 ARG 0.004 0.000 ARG B 839 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 123 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 LEU cc_start: 0.1544 (OUTLIER) cc_final: 0.1279 (tt) REVERT: B 37 HIS cc_start: 0.5798 (OUTLIER) cc_final: 0.5480 (t70) REVERT: B 38 HIS cc_start: 0.6853 (m-70) cc_final: 0.6531 (m-70) REVERT: B 62 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7567 (tt) REVERT: B 380 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6358 (tt) REVERT: B 451 ASP cc_start: 0.2002 (OUTLIER) cc_final: -0.1692 (t0) REVERT: B 492 MET cc_start: 0.6808 (ptm) cc_final: 0.6452 (ptm) REVERT: B 794 MET cc_start: 0.5072 (mtp) cc_final: 0.4646 (mtm) REVERT: B 827 TRP cc_start: 0.7497 (t60) cc_final: 0.7135 (t-100) outliers start: 45 outliers final: 25 residues processed: 150 average time/residue: 0.1636 time to fit residues: 33.3879 Evaluate side-chains 150 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 32 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 6466 Z= 0.221 Angle : 0.689 10.497 8830 Z= 0.327 Chirality : 0.041 0.169 1088 Planarity : 0.005 0.041 1123 Dihedral : 4.320 23.929 906 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.66 % Allowed : 26.22 % Favored : 70.12 % 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: 0.38 (0.30), residues: 850 helix: 1.35 (0.22), residues: 574 sheet: -0.39 (0.92), residues: 38 loop : -2.45 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 827 HIS 0.001 0.000 HIS B 358 PHE 0.020 0.001 PHE B 392 TYR 0.008 0.001 TYR B 353 ARG 0.004 0.000 ARG B 839 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: B 380 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6248 (tt) REVERT: B 492 MET cc_start: 0.6637 (ptm) cc_final: 0.6350 (ptm) REVERT: B 794 MET cc_start: 0.4856 (mtp) cc_final: 0.4460 (mtm) REVERT: B 827 TRP cc_start: 0.7427 (t60) cc_final: 0.7137 (t-100) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.1646 time to fit residues: 31.5907 Evaluate side-chains 137 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6466 Z= 0.206 Angle : 0.708 10.597 8830 Z= 0.337 Chirality : 0.042 0.149 1088 Planarity : 0.005 0.041 1123 Dihedral : 4.323 26.619 906 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.20 % Allowed : 26.98 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 850 helix: 1.44 (0.22), residues: 569 sheet: -0.46 (0.92), residues: 38 loop : -2.31 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 827 HIS 0.006 0.001 HIS B 37 PHE 0.021 0.001 PHE B 720 TYR 0.011 0.001 TYR B 353 ARG 0.003 0.000 ARG B 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7470 (mtm-85) REVERT: B 380 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6273 (tt) REVERT: B 428 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.2308 (tp) REVERT: B 451 ASP cc_start: 0.1872 (OUTLIER) cc_final: -0.1903 (t0) REVERT: B 492 MET cc_start: 0.6692 (ptm) cc_final: 0.6402 (ptm) REVERT: B 768 MET cc_start: 0.6827 (pmm) cc_final: 0.6271 (pmm) REVERT: B 793 VAL cc_start: 0.6448 (OUTLIER) cc_final: 0.6028 (t) REVERT: B 794 MET cc_start: 0.4929 (mtp) cc_final: 0.4270 (mtm) REVERT: B 827 TRP cc_start: 0.7456 (t60) cc_final: 0.7209 (t-100) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.1563 time to fit residues: 28.4031 Evaluate side-chains 138 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6466 Z= 0.256 Angle : 0.762 9.065 8830 Z= 0.366 Chirality : 0.043 0.160 1088 Planarity : 0.005 0.044 1123 Dihedral : 4.568 29.578 906 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.20 % Allowed : 27.90 % Favored : 68.90 % 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: 0.21 (0.30), residues: 850 helix: 1.16 (0.22), residues: 576 sheet: -0.66 (0.91), residues: 38 loop : -2.32 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 827 HIS 0.004 0.001 HIS B 453 PHE 0.025 0.001 PHE B 720 TYR 0.014 0.002 TYR B 353 ARG 0.004 0.000 ARG B 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 380 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6368 (tt) REVERT: B 428 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.2475 (tp) REVERT: B 451 ASP cc_start: 0.2006 (OUTLIER) cc_final: -0.1678 (t0) REVERT: B 492 MET cc_start: 0.6774 (ptm) cc_final: 0.6532 (ptm) REVERT: B 768 MET cc_start: 0.6920 (pmm) cc_final: 0.6437 (pmm) REVERT: B 827 TRP cc_start: 0.7588 (t60) cc_final: 0.7386 (t60) outliers start: 21 outliers final: 17 residues processed: 135 average time/residue: 0.1808 time to fit residues: 34.0632 Evaluate side-chains 142 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 84 optimal weight: 0.0980 chunk 77 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6466 Z= 0.281 Angle : 0.787 10.204 8830 Z= 0.379 Chirality : 0.044 0.149 1088 Planarity : 0.005 0.049 1123 Dihedral : 4.735 29.836 906 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.66 % Allowed : 27.90 % Favored : 68.45 % 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 (0.30), residues: 850 helix: 0.92 (0.22), residues: 585 sheet: -0.91 (0.87), residues: 38 loop : -2.48 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 827 HIS 0.003 0.001 HIS B 711 PHE 0.024 0.002 PHE B 720 TYR 0.013 0.002 TYR B 353 ARG 0.004 0.000 ARG B 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7415 (mtm180) REVERT: B 380 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6378 (tt) REVERT: B 428 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.2349 (tp) REVERT: B 451 ASP cc_start: 0.2092 (OUTLIER) cc_final: -0.1588 (t0) REVERT: B 492 MET cc_start: 0.6828 (ptm) cc_final: 0.6529 (ptm) REVERT: B 768 MET cc_start: 0.6958 (pmm) cc_final: 0.6548 (pmm) REVERT: B 794 MET cc_start: 0.4846 (mtp) cc_final: 0.4460 (mtm) REVERT: B 827 TRP cc_start: 0.7574 (t60) cc_final: 0.7355 (t60) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.1646 time to fit residues: 29.5974 Evaluate side-chains 136 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 69 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 50.0000 chunk 3 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.227737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.205188 restraints weight = 9062.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.209759 restraints weight = 5370.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.212885 restraints weight = 3561.449| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6466 Z= 0.228 Angle : 0.760 9.835 8830 Z= 0.364 Chirality : 0.043 0.153 1088 Planarity : 0.005 0.043 1123 Dihedral : 4.613 29.480 906 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.20 % Allowed : 28.20 % Favored : 68.60 % 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: 0.14 (0.30), residues: 850 helix: 1.13 (0.22), residues: 579 sheet: -0.84 (0.87), residues: 38 loop : -2.41 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 827 HIS 0.003 0.001 HIS B 711 PHE 0.024 0.001 PHE B 720 TYR 0.012 0.001 TYR B 353 ARG 0.004 0.000 ARG B 621 =============================================================================== Job complete usr+sys time: 1476.55 seconds wall clock time: 27 minutes 29.42 seconds (1649.42 seconds total)