Starting phenix.real_space_refine on Sat Jul 20 11:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqu_18605/07_2024/8qqu_18605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqu_18605/07_2024/8qqu_18605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqu_18605/07_2024/8qqu_18605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqu_18605/07_2024/8qqu_18605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqu_18605/07_2024/8qqu_18605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqu_18605/07_2024/8qqu_18605.cif" } resolution = 2.9 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= 0.006 sd= 0.204 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 38 5.16 5 C 6634 2.51 5 N 1904 2.21 5 O 2107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10715 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4096 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 21, 'TRANS': 497} Chain: "D" Number of atoms: 5963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5963 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 26, 'TRANS': 727} Chain breaks: 1 Chain: "E" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "F" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 7.13, per 1000 atoms: 0.67 Number of scatterers: 10715 At special positions: 0 Unit cell: (137.058, 101.716, 119.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 32 15.00 O 2107 8.00 N 1904 7.00 C 6634 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 1.9 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 49.6% alpha, 14.4% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.694A pdb=" N HIS C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 136 No H-bonds generated for 'chain 'C' and resid 135 through 136' Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.503A pdb=" N LYS C 140 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.921A pdb=" N HIS C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.657A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.919A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.951A pdb=" N TYR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.848A pdb=" N HIS D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.580A pdb=" N ALA D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.724A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 Processing helix chain 'D' and resid 279 through 301 Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.628A pdb=" N LYS D 305 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 364 removed outlier: 4.590A pdb=" N SER D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 385 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.601A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 3.617A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 576 through 597 Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.670A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 622 removed outlier: 3.607A pdb=" N LEU D 620 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 622' Processing helix chain 'D' and resid 622 through 640 removed outlier: 3.631A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 removed outlier: 3.600A pdb=" N THR D 683 " --> pdb=" O HIS D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.579A pdb=" N MET D 755 " --> pdb=" O TRP D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 785 through 801 Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.676A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'C' and resid 327 through 333 Processing sheet with id=AA6, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.603A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 303 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 292 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 306 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AA9, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.545A pdb=" N ARG D 136 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR D 145 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 129 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 168 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.506A pdb=" N LYS D 247 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.536A pdb=" N GLY D 251 " --> pdb=" O LYS D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AB4, first strand: chain 'D' and resid 565 through 567 removed outlier: 4.203A pdb=" N ARG D 712 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 647 through 654 removed outlier: 3.574A pdb=" N LEU D 659 " --> pdb=" O ASN D 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 2243 1.45 - 1.57: 6121 1.57 - 1.69: 62 1.69 - 1.81: 70 Bond restraints: 10959 Sorted by residual: bond pdb=" C HIS C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 7.00e+00 bond pdb=" C1' DT E 14 " pdb=" N1 DT E 14 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" C1' DT E 13 " pdb=" N1 DT E 13 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.84e+00 bond pdb=" C1' DT E 15 " pdb=" N1 DT E 15 " ideal model delta sigma weight residual 1.490 1.548 -0.058 3.00e-02 1.11e+03 3.76e+00 ... (remaining 10954 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.43: 457 106.43 - 113.34: 5905 113.34 - 120.25: 4047 120.25 - 127.16: 4347 127.16 - 134.07: 182 Bond angle restraints: 14938 Sorted by residual: angle pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " pdb=" P DT E 15 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C LYS C 140 " pdb=" N GLU C 141 " pdb=" CA GLU C 141 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.22e+00 angle pdb=" C3' DT E 6 " pdb=" C2' DT E 6 " pdb=" C1' DT E 6 " ideal model delta sigma weight residual 101.60 105.52 -3.92 1.50e+00 4.44e-01 6.83e+00 angle pdb=" C3' DA F 9 " pdb=" C2' DA F 9 " pdb=" C1' DA F 9 " ideal model delta sigma weight residual 101.60 105.43 -3.83 1.50e+00 4.44e-01 6.52e+00 angle pdb=" CA GLU C 139 " pdb=" CB GLU C 139 " pdb=" CG GLU C 139 " ideal model delta sigma weight residual 114.10 118.91 -4.81 2.00e+00 2.50e-01 5.77e+00 ... (remaining 14933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 6456 31.52 - 63.04: 191 63.04 - 94.57: 4 94.57 - 126.09: 0 126.09 - 157.61: 2 Dihedral angle restraints: 6653 sinusoidal: 2973 harmonic: 3680 Sorted by residual: dihedral pdb=" CA GLY C 31 " pdb=" C GLY C 31 " pdb=" N ARG C 32 " pdb=" CA ARG C 32 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU D 355 " pdb=" C GLU D 355 " pdb=" N LEU D 356 " pdb=" CA LEU D 356 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C4' DT E 14 " pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " pdb=" P DT E 15 " ideal model delta sinusoidal sigma weight residual 220.00 62.39 157.61 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 6650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1102 0.037 - 0.075: 418 0.075 - 0.112: 86 0.112 - 0.150: 61 0.150 - 0.187: 8 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1672 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 163 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 164 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 31 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLY C 31 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY C 31 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG C 32 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 786 " -0.028 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO D 787 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 787 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 787 " -0.023 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 156 2.67 - 3.23: 9606 3.23 - 3.78: 16084 3.78 - 4.34: 22447 4.34 - 4.90: 37372 Nonbonded interactions: 85665 Sorted by model distance: nonbonded pdb=" O LEU C 320 " pdb=" OG1 THR C 324 " model vdw 2.111 2.440 nonbonded pdb=" O LEU D 509 " pdb=" OG1 THR D 512 " model vdw 2.226 2.440 nonbonded pdb=" NH1 ARG D 394 " pdb=" O GLU D 412 " model vdw 2.244 2.520 nonbonded pdb=" OH TYR D 184 " pdb=" OD2 ASP D 214 " model vdw 2.262 2.440 nonbonded pdb=" O HIS D 505 " pdb=" OG1 THR D 508 " model vdw 2.269 2.440 ... (remaining 85660 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 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: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.550 Find NCS groups from input model: 0.090 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.004 0.066 10959 Z= 0.277 Angle : 0.673 6.541 14938 Z= 0.366 Chirality : 0.046 0.187 1675 Planarity : 0.004 0.054 1846 Dihedral : 13.967 157.611 4283 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1267 helix: 1.56 (0.20), residues: 582 sheet: -1.61 (0.36), residues: 189 loop : -1.13 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 170 HIS 0.004 0.001 HIS C 378 PHE 0.016 0.002 PHE D 243 TYR 0.011 0.001 TYR C 321 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.176 Fit side-chains REVERT: C 231 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7531 (mp0) REVERT: C 341 GLN cc_start: 0.8005 (mt0) cc_final: 0.7783 (mt0) REVERT: C 479 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7446 (mttm) REVERT: D 45 ASP cc_start: 0.7508 (t0) cc_final: 0.7266 (t0) REVERT: D 124 ASN cc_start: 0.8112 (p0) cc_final: 0.7834 (t0) REVERT: D 247 LYS cc_start: 0.7619 (tttp) cc_final: 0.7391 (ptpt) REVERT: D 406 LYS cc_start: 0.8142 (mttt) cc_final: 0.7885 (mtmt) REVERT: D 731 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7707 (mtp180) REVERT: D 754 THR cc_start: 0.8333 (p) cc_final: 0.8064 (p) REVERT: D 771 ILE cc_start: 0.8480 (mt) cc_final: 0.8073 (pp) outliers start: 0 outliers final: 1 residues processed: 268 average time/residue: 1.4747 time to fit residues: 419.0756 Evaluate side-chains 141 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS C 94 GLN C 186 ASN C 269 ASN C 327 GLN C 413 ASN C 471 HIS D 141 HIS D 237 HIS D 556 GLN D 654 ASN D 669 HIS D 721 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10959 Z= 0.390 Angle : 0.617 6.893 14938 Z= 0.332 Chirality : 0.045 0.151 1675 Planarity : 0.005 0.044 1846 Dihedral : 15.114 167.123 1783 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 13.07 % 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: 0.33 (0.23), residues: 1267 helix: 1.77 (0.21), residues: 597 sheet: -1.30 (0.35), residues: 196 loop : -1.10 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 170 HIS 0.010 0.002 HIS D 281 PHE 0.014 0.002 PHE D 243 TYR 0.014 0.002 TYR C 321 ARG 0.005 0.001 ARG D 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.130 Fit side-chains REVERT: C 231 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7532 (mp0) REVERT: C 440 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: C 479 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7402 (mttm) REVERT: D 45 ASP cc_start: 0.7657 (t0) cc_final: 0.7395 (t0) REVERT: D 147 HIS cc_start: 0.7631 (m-70) cc_final: 0.7333 (m-70) REVERT: D 166 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6323 (tmm) REVERT: D 247 LYS cc_start: 0.7732 (tttp) cc_final: 0.7355 (ptpt) REVERT: D 275 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: D 399 ASP cc_start: 0.7255 (m-30) cc_final: 0.6916 (t70) REVERT: D 406 LYS cc_start: 0.8241 (mttt) cc_final: 0.7891 (mtmt) REVERT: D 538 LYS cc_start: 0.8944 (tttt) cc_final: 0.8721 (tttm) REVERT: D 624 GLN cc_start: 0.7270 (mp10) cc_final: 0.6941 (mp10) REVERT: D 731 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7869 (mtp180) REVERT: D 771 ILE cc_start: 0.8466 (mt) cc_final: 0.8225 (pp) outliers start: 32 outliers final: 10 residues processed: 160 average time/residue: 1.4368 time to fit residues: 245.5665 Evaluate side-chains 131 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 728 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS D 141 HIS D 215 HIS D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10959 Z= 0.159 Angle : 0.488 6.624 14938 Z= 0.265 Chirality : 0.040 0.183 1675 Planarity : 0.003 0.053 1846 Dihedral : 14.449 178.602 1780 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.43 % Allowed : 15.13 % Favored : 82.45 % 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: 0.89 (0.24), residues: 1267 helix: 2.32 (0.21), residues: 593 sheet: -0.91 (0.35), residues: 196 loop : -0.97 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 170 HIS 0.006 0.001 HIS C 471 PHE 0.012 0.001 PHE D 243 TYR 0.011 0.001 TYR D 184 ARG 0.006 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.7795 (m-30) cc_final: 0.7584 (m-30) REVERT: C 231 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7513 (mp0) REVERT: C 440 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6885 (pt0) REVERT: D 124 ASN cc_start: 0.8025 (p0) cc_final: 0.7583 (t0) REVERT: D 247 LYS cc_start: 0.7745 (tttp) cc_final: 0.7416 (ptpt) REVERT: D 399 ASP cc_start: 0.7197 (m-30) cc_final: 0.6898 (t0) REVERT: D 538 LYS cc_start: 0.8920 (tttt) cc_final: 0.8642 (ttmm) REVERT: D 596 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7029 (mtp180) REVERT: D 720 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7663 (pp20) REVERT: D 771 ILE cc_start: 0.8450 (mt) cc_final: 0.8207 (pp) outliers start: 26 outliers final: 5 residues processed: 152 average time/residue: 1.3578 time to fit residues: 220.9681 Evaluate side-chains 125 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 596 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN D 55 HIS D 232 ASN D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10959 Z= 0.198 Angle : 0.491 6.005 14938 Z= 0.266 Chirality : 0.040 0.139 1675 Planarity : 0.004 0.054 1846 Dihedral : 14.441 178.121 1780 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.45 % Allowed : 15.31 % Favored : 81.23 % 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: 1.04 (0.24), residues: 1267 helix: 2.41 (0.21), residues: 594 sheet: -0.81 (0.35), residues: 202 loop : -0.87 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 PHE 0.015 0.001 PHE D 243 TYR 0.007 0.001 TYR C 63 ARG 0.007 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.7778 (m-30) cc_final: 0.7563 (m-30) REVERT: C 231 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7532 (mp0) REVERT: C 440 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: D 124 ASN cc_start: 0.8129 (p0) cc_final: 0.7730 (t0) REVERT: D 202 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7348 (t) REVERT: D 275 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: D 399 ASP cc_start: 0.7170 (m-30) cc_final: 0.6857 (t0) REVERT: D 531 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: D 538 LYS cc_start: 0.9015 (tttt) cc_final: 0.8704 (ttmm) REVERT: D 596 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7012 (mtp180) REVERT: D 652 HIS cc_start: 0.7252 (t-90) cc_final: 0.6964 (t-90) REVERT: D 771 ILE cc_start: 0.8564 (mt) cc_final: 0.8289 (pp) outliers start: 37 outliers final: 12 residues processed: 146 average time/residue: 1.3102 time to fit residues: 205.5951 Evaluate side-chains 131 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10959 Z= 0.267 Angle : 0.531 9.738 14938 Z= 0.285 Chirality : 0.042 0.192 1675 Planarity : 0.004 0.056 1846 Dihedral : 14.542 176.466 1780 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.73 % Allowed : 15.13 % Favored : 81.14 % 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: 0.95 (0.24), residues: 1267 helix: 2.33 (0.21), residues: 597 sheet: -0.78 (0.35), residues: 202 loop : -0.97 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 PHE 0.016 0.002 PHE D 243 TYR 0.010 0.001 TYR C 63 ARG 0.008 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 1.244 Fit side-chains REVERT: C 72 ASP cc_start: 0.7831 (m-30) cc_final: 0.7609 (m-30) REVERT: C 231 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7562 (mp0) REVERT: C 440 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6883 (pt0) REVERT: D 124 ASN cc_start: 0.8165 (p0) cc_final: 0.7722 (t0) REVERT: D 170 TRP cc_start: 0.6509 (OUTLIER) cc_final: 0.5465 (m-10) REVERT: D 275 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: D 399 ASP cc_start: 0.7192 (m-30) cc_final: 0.6843 (t0) REVERT: D 531 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: D 553 ASP cc_start: 0.7683 (m-30) cc_final: 0.7438 (m-30) REVERT: D 596 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7017 (mtp180) REVERT: D 652 HIS cc_start: 0.7351 (t-90) cc_final: 0.7084 (t-90) REVERT: D 698 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6173 (mmt90) REVERT: D 771 ILE cc_start: 0.8487 (mt) cc_final: 0.8235 (pp) outliers start: 40 outliers final: 16 residues processed: 148 average time/residue: 1.3519 time to fit residues: 214.6641 Evaluate side-chains 136 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10959 Z= 0.270 Angle : 0.539 8.353 14938 Z= 0.288 Chirality : 0.042 0.175 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.567 175.709 1780 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.04 % Allowed : 14.38 % Favored : 80.58 % 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: 0.93 (0.24), residues: 1267 helix: 2.32 (0.21), residues: 591 sheet: -0.72 (0.35), residues: 202 loop : -0.99 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 PHE 0.017 0.002 PHE D 243 TYR 0.010 0.001 TYR C 63 ARG 0.010 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 118 time to evaluate : 1.211 Fit side-chains REVERT: C 72 ASP cc_start: 0.7874 (m-30) cc_final: 0.7640 (m-30) REVERT: C 231 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7562 (mp0) REVERT: C 440 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: D 124 ASN cc_start: 0.8212 (p0) cc_final: 0.7798 (t0) REVERT: D 170 TRP cc_start: 0.6568 (OUTLIER) cc_final: 0.5503 (m-10) REVERT: D 275 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: D 399 ASP cc_start: 0.7217 (m-30) cc_final: 0.6879 (t0) REVERT: D 531 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: D 553 ASP cc_start: 0.7661 (m-30) cc_final: 0.7414 (m-30) REVERT: D 596 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7020 (mtp180) REVERT: D 624 GLN cc_start: 0.7194 (mp10) cc_final: 0.6954 (mp10) REVERT: D 652 HIS cc_start: 0.7390 (t-90) cc_final: 0.7132 (t-90) REVERT: D 698 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6457 (mmt90) REVERT: D 745 MET cc_start: 0.9158 (mtp) cc_final: 0.8952 (mtm) REVERT: D 771 ILE cc_start: 0.8502 (mt) cc_final: 0.8244 (pp) outliers start: 54 outliers final: 20 residues processed: 158 average time/residue: 1.3367 time to fit residues: 226.4879 Evaluate side-chains 138 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN D 55 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10959 Z= 0.186 Angle : 0.505 12.490 14938 Z= 0.269 Chirality : 0.040 0.165 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.350 177.183 1780 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.27 % Allowed : 16.81 % Favored : 79.93 % 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: 1.07 (0.24), residues: 1267 helix: 2.41 (0.21), residues: 598 sheet: -0.54 (0.36), residues: 202 loop : -0.99 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 PHE 0.015 0.001 PHE D 243 TYR 0.009 0.001 TYR D 184 ARG 0.010 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.269 Fit side-chains REVERT: C 72 ASP cc_start: 0.7788 (m-30) cc_final: 0.7580 (m-30) REVERT: C 231 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7564 (mp0) REVERT: C 440 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: D 124 ASN cc_start: 0.8164 (p0) cc_final: 0.7649 (t0) REVERT: D 202 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7289 (t) REVERT: D 275 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: D 399 ASP cc_start: 0.7204 (m-30) cc_final: 0.6914 (t0) REVERT: D 531 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: D 553 ASP cc_start: 0.7707 (m-30) cc_final: 0.7449 (m-30) REVERT: D 596 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7009 (mtp180) REVERT: D 624 GLN cc_start: 0.7197 (mp10) cc_final: 0.6979 (mp10) REVERT: D 652 HIS cc_start: 0.7387 (t-90) cc_final: 0.7111 (t-90) REVERT: D 771 ILE cc_start: 0.8488 (mt) cc_final: 0.8249 (pp) outliers start: 35 outliers final: 15 residues processed: 141 average time/residue: 1.2496 time to fit residues: 190.0220 Evaluate side-chains 132 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10959 Z= 0.247 Angle : 0.535 11.940 14938 Z= 0.285 Chirality : 0.042 0.170 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.487 176.006 1780 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.55 % Allowed : 16.34 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1267 helix: 2.32 (0.21), residues: 598 sheet: -0.51 (0.36), residues: 202 loop : -1.03 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 PHE 0.016 0.002 PHE D 243 TYR 0.010 0.001 TYR C 63 ARG 0.011 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.149 Fit side-chains REVERT: C 72 ASP cc_start: 0.7817 (m-30) cc_final: 0.7602 (m-30) REVERT: C 231 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7566 (mp0) REVERT: C 401 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.7576 (Cg_exo) REVERT: C 440 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6875 (pt0) REVERT: D 124 ASN cc_start: 0.8169 (p0) cc_final: 0.7622 (t0) REVERT: D 202 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7319 (t) REVERT: D 275 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: D 399 ASP cc_start: 0.7266 (m-30) cc_final: 0.6971 (t70) REVERT: D 531 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: D 553 ASP cc_start: 0.7700 (m-30) cc_final: 0.7443 (m-30) REVERT: D 596 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7005 (mtp180) REVERT: D 624 GLN cc_start: 0.7203 (mp10) cc_final: 0.6964 (mp10) REVERT: D 652 HIS cc_start: 0.7434 (t-90) cc_final: 0.7143 (t-90) REVERT: D 771 ILE cc_start: 0.8464 (mt) cc_final: 0.8263 (pp) outliers start: 38 outliers final: 19 residues processed: 147 average time/residue: 1.3819 time to fit residues: 218.1129 Evaluate side-chains 136 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10959 Z= 0.190 Angle : 0.526 11.432 14938 Z= 0.279 Chirality : 0.041 0.192 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.347 177.058 1780 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.24 % Allowed : 17.93 % Favored : 79.83 % 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: 1267 helix: 2.37 (0.21), residues: 598 sheet: -0.41 (0.36), residues: 199 loop : -0.94 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 PHE 0.015 0.001 PHE D 243 TYR 0.008 0.001 TYR C 21 ARG 0.013 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.066 Fit side-chains REVERT: C 61 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7976 (mppt) REVERT: C 72 ASP cc_start: 0.7749 (m-30) cc_final: 0.7544 (m-30) REVERT: C 231 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7557 (mp0) REVERT: C 440 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6870 (pt0) REVERT: D 124 ASN cc_start: 0.8136 (p0) cc_final: 0.7600 (t0) REVERT: D 202 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7288 (t) REVERT: D 275 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: D 399 ASP cc_start: 0.7268 (m-30) cc_final: 0.7011 (t70) REVERT: D 531 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: D 553 ASP cc_start: 0.7712 (m-30) cc_final: 0.7456 (m-30) REVERT: D 581 GLU cc_start: 0.7911 (tt0) cc_final: 0.7617 (tt0) REVERT: D 596 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6990 (mtp180) REVERT: D 624 GLN cc_start: 0.7230 (mp10) cc_final: 0.6986 (mp10) REVERT: D 652 HIS cc_start: 0.7400 (t-90) cc_final: 0.7134 (t-90) REVERT: D 758 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8059 (mm-30) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 1.3274 time to fit residues: 199.7295 Evaluate side-chains 133 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10959 Z= 0.355 Angle : 0.611 11.248 14938 Z= 0.322 Chirality : 0.044 0.183 1675 Planarity : 0.005 0.060 1846 Dihedral : 14.780 173.925 1780 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.33 % Allowed : 18.21 % Favored : 79.46 % 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: 0.75 (0.23), residues: 1267 helix: 2.09 (0.21), residues: 597 sheet: -0.54 (0.36), residues: 202 loop : -1.12 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 170 HIS 0.009 0.001 HIS D 281 PHE 0.018 0.002 PHE D 243 TYR 0.013 0.002 TYR C 63 ARG 0.013 0.001 ARG D 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.411 Fit side-chains REVERT: C 61 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7989 (mppt) REVERT: C 72 ASP cc_start: 0.7874 (m-30) cc_final: 0.7652 (m-30) REVERT: C 163 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8699 (mt) REVERT: C 231 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7551 (mp0) REVERT: C 401 PRO cc_start: 0.7983 (Cg_endo) cc_final: 0.7703 (Cg_exo) REVERT: C 440 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6864 (pt0) REVERT: D 124 ASN cc_start: 0.8208 (p0) cc_final: 0.7634 (t0) REVERT: D 275 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: D 399 ASP cc_start: 0.7377 (m-30) cc_final: 0.7045 (t70) REVERT: D 531 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: D 553 ASP cc_start: 0.7715 (m-30) cc_final: 0.7461 (m-30) REVERT: D 596 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6990 (mtp180) REVERT: D 597 MET cc_start: 0.8324 (mtp) cc_final: 0.8108 (mtp) REVERT: D 624 GLN cc_start: 0.7191 (mp10) cc_final: 0.6937 (mp10) REVERT: D 704 ASP cc_start: 0.7840 (p0) cc_final: 0.7354 (p0) REVERT: D 745 MET cc_start: 0.9173 (mtp) cc_final: 0.8961 (mtm) outliers start: 25 outliers final: 13 residues processed: 133 average time/residue: 1.3337 time to fit residues: 191.2920 Evaluate side-chains 128 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117597 restraints weight = 13824.296| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.77 r_work: 0.3271 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10959 Z= 0.206 Angle : 0.557 11.510 14938 Z= 0.294 Chirality : 0.041 0.176 1675 Planarity : 0.004 0.065 1846 Dihedral : 14.630 175.511 1780 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.43 % Allowed : 18.39 % Favored : 79.18 % 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 (0.24), residues: 1267 helix: 2.21 (0.21), residues: 597 sheet: -0.50 (0.36), residues: 202 loop : -1.04 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 415 HIS 0.006 0.001 HIS D 281 PHE 0.015 0.001 PHE D 262 TYR 0.009 0.001 TYR D 184 ARG 0.013 0.000 ARG D 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.02 seconds wall clock time: 77 minutes 27.89 seconds (4647.89 seconds total)