Starting phenix.real_space_refine on Mon Jul 28 21:47:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqu_18605/07_2025/8qqu_18605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqu_18605/07_2025/8qqu_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/cci-nas-00/data/ceres_data/8qqu_18605/07_2025/8qqu_18605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqu_18605/07_2025/8qqu_18605.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqu_18605/07_2025/8qqu_18605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqu_18605/07_2025/8qqu_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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.76, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 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: 3.45 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: 3.76 Time building geometry restraints manager: 3.28 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: 0.00 - 1.31: 14197 1.31 - 2.62: 604 2.62 - 3.92: 77 3.92 - 5.23: 45 5.23 - 6.54: 15 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 3.040 nonbonded pdb=" O LEU D 509 " pdb=" OG1 THR D 512 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG D 394 " pdb=" O GLU D 412 " model vdw 2.244 3.120 nonbonded pdb=" OH TYR D 184 " pdb=" OD2 ASP D 214 " model vdw 2.262 3.040 nonbonded pdb=" O HIS D 505 " pdb=" OG1 THR D 508 " model vdw 2.269 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.260 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.010 Find NCS groups from input model: 0.080 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.140 ------------------------------------------------------------------------------- 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= 0.186 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 Details of bonding type rmsd hydrogen bonds : bond 0.16858 ( 566) hydrogen bonds : angle 6.65200 ( 1608) covalent geometry : bond 0.00429 (10959) covalent geometry : angle 0.67265 (14938) *********************** 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 to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.375 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: 1.6599 time to fit residues: 471.8371 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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: 0.9980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 269 ASN C 327 GLN C 413 ASN C 471 HIS D 141 HIS D 215 HIS D 237 HIS D 556 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN D 669 HIS D 721 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114651 restraints weight = 13734.374| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.75 r_work: 0.3255 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10959 Z= 0.216 Angle : 0.595 6.363 14938 Z= 0.322 Chirality : 0.044 0.151 1675 Planarity : 0.004 0.043 1846 Dihedral : 15.037 167.949 1783 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.71 % Allowed : 12.70 % Favored : 84.59 % 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: 0.41 (0.23), residues: 1267 helix: 1.86 (0.21), residues: 596 sheet: -1.25 (0.35), residues: 196 loop : -1.08 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 170 HIS 0.008 0.001 HIS D 281 PHE 0.013 0.002 PHE D 169 TYR 0.013 0.002 TYR C 321 ARG 0.006 0.001 ARG D 394 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 566) hydrogen bonds : angle 4.83401 ( 1608) covalent geometry : bond 0.00515 (10959) covalent geometry : angle 0.59467 (14938) *********************** 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 180 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.238 Fit side-chains REVERT: C 231 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7773 (mp0) REVERT: C 440 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7082 (pt0) REVERT: C 479 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7516 (mttm) REVERT: D 147 HIS cc_start: 0.7672 (m-70) cc_final: 0.7351 (m-70) REVERT: D 166 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6432 (tmm) REVERT: D 247 LYS cc_start: 0.7992 (tttp) cc_final: 0.7513 (ptpt) REVERT: D 399 ASP cc_start: 0.7500 (m-30) cc_final: 0.7044 (t70) REVERT: D 406 LYS cc_start: 0.8361 (mttt) cc_final: 0.8050 (mtmt) REVERT: D 624 GLN cc_start: 0.7417 (mp10) cc_final: 0.7059 (mp10) REVERT: D 731 ARG cc_start: 0.8351 (mtp180) cc_final: 0.8085 (mtp180) REVERT: D 752 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8076 (pt0) outliers start: 29 outliers final: 10 residues processed: 167 average time/residue: 1.6259 time to fit residues: 288.8139 Evaluate side-chains 132 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 GLU 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 459 ASP Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 752 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS C 341 GLN D 37 HIS D 141 HIS D 556 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120215 restraints weight = 13884.468| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.77 r_work: 0.3315 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10959 Z= 0.120 Angle : 0.499 6.448 14938 Z= 0.272 Chirality : 0.040 0.147 1675 Planarity : 0.004 0.053 1846 Dihedral : 14.530 179.014 1780 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.61 % Allowed : 14.01 % Favored : 83.38 % 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: 0.81 (0.24), residues: 1267 helix: 2.22 (0.21), residues: 597 sheet: -0.89 (0.36), residues: 196 loop : -1.02 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 PHE 0.012 0.001 PHE D 243 TYR 0.007 0.001 TYR C 63 ARG 0.006 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 566) hydrogen bonds : angle 4.40529 ( 1608) covalent geometry : bond 0.00271 (10959) covalent geometry : angle 0.49895 (14938) *********************** 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 164 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.240 Fit side-chains REVERT: C 6 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6814 (ttp-110) REVERT: C 72 ASP cc_start: 0.7666 (m-30) cc_final: 0.7441 (m-30) REVERT: C 231 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7613 (mp0) REVERT: C 285 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7767 (mtp85) REVERT: C 440 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7075 (pt0) REVERT: D 124 ASN cc_start: 0.8144 (p0) cc_final: 0.7736 (t0) REVERT: D 147 HIS cc_start: 0.7628 (m-70) cc_final: 0.7366 (m-70) REVERT: D 247 LYS cc_start: 0.7946 (tttp) cc_final: 0.7459 (ptpt) REVERT: D 399 ASP cc_start: 0.7373 (m-30) cc_final: 0.6970 (t70) REVERT: D 758 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8235 (mm-30) outliers start: 28 outliers final: 7 residues processed: 153 average time/residue: 1.3705 time to fit residues: 224.7737 Evaluate side-chains 124 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR 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 D residue 45 ASP Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 ASN D 37 HIS D 55 HIS D 232 ASN D 556 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120452 restraints weight = 13877.395| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.76 r_work: 0.3297 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10959 Z= 0.117 Angle : 0.497 9.927 14938 Z= 0.269 Chirality : 0.040 0.150 1675 Planarity : 0.004 0.054 1846 Dihedral : 14.408 178.809 1780 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 15.50 % Favored : 82.17 % 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: 1.03 (0.24), residues: 1267 helix: 2.39 (0.21), residues: 596 sheet: -0.77 (0.36), residues: 202 loop : -0.89 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 170 HIS 0.005 0.001 HIS D 55 PHE 0.015 0.001 PHE D 660 TYR 0.007 0.001 TYR C 86 ARG 0.006 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 566) hydrogen bonds : angle 4.23874 ( 1608) covalent geometry : bond 0.00265 (10959) covalent geometry : angle 0.49659 (14938) *********************** 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 145 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.210 Fit side-chains REVERT: C 72 ASP cc_start: 0.7669 (m-30) cc_final: 0.7460 (m-30) REVERT: C 231 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7715 (mp0) REVERT: C 440 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7055 (pt0) REVERT: D 124 ASN cc_start: 0.8261 (p0) cc_final: 0.7924 (t0) REVERT: D 262 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.5956 (p90) REVERT: D 399 ASP cc_start: 0.7432 (m-30) cc_final: 0.7067 (t0) REVERT: D 531 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: D 581 GLU cc_start: 0.8179 (tt0) cc_final: 0.7881 (tt0) REVERT: D 596 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7272 (mtp180) REVERT: D 758 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8238 (mm-30) outliers start: 25 outliers final: 6 residues processed: 138 average time/residue: 1.4044 time to fit residues: 207.8469 Evaluate side-chains 121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR 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 173 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 444 LEU 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 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 124 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN D 37 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.149102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122807 restraints weight = 13839.190| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.77 r_work: 0.3345 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 10959 Z= 0.106 Angle : 0.477 7.946 14938 Z= 0.258 Chirality : 0.040 0.166 1675 Planarity : 0.003 0.055 1846 Dihedral : 14.200 179.034 1780 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.80 % Allowed : 14.94 % Favored : 82.26 % 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: 1.25 (0.24), residues: 1267 helix: 2.54 (0.21), residues: 595 sheet: -0.49 (0.36), residues: 202 loop : -0.83 (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 0.014 0.001 PHE D 243 TYR 0.006 0.001 TYR D 145 ARG 0.010 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 566) hydrogen bonds : angle 4.06392 ( 1608) covalent geometry : bond 0.00233 (10959) covalent geometry : angle 0.47670 (14938) *********************** 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 to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.136 Fit side-chains REVERT: C 231 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7698 (mp0) REVERT: C 440 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7129 (pt0) REVERT: D 182 PHE cc_start: 0.7804 (m-80) cc_final: 0.7543 (m-10) REVERT: D 399 ASP cc_start: 0.7386 (m-30) cc_final: 0.7065 (t0) REVERT: D 518 MET cc_start: 0.8795 (mtt) cc_final: 0.8428 (mtp) REVERT: D 531 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: D 581 GLU cc_start: 0.8156 (tt0) cc_final: 0.7906 (tt0) REVERT: D 596 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7256 (mtp180) REVERT: D 758 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8208 (mm-30) outliers start: 30 outliers final: 7 residues processed: 152 average time/residue: 1.4907 time to fit residues: 242.9413 Evaluate side-chains 123 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 440 GLU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 205 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 0.0980 chunk 108 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 37 HIS D 232 ASN D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121863 restraints weight = 13990.277| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.78 r_work: 0.3344 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 10959 Z= 0.107 Angle : 0.478 6.662 14938 Z= 0.259 Chirality : 0.040 0.155 1675 Planarity : 0.004 0.055 1846 Dihedral : 14.163 178.720 1780 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 16.71 % 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: 1.36 (0.24), residues: 1267 helix: 2.62 (0.21), residues: 594 sheet: -0.36 (0.37), residues: 205 loop : -0.79 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 PHE 0.014 0.001 PHE D 243 TYR 0.010 0.001 TYR D 145 ARG 0.010 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 566) hydrogen bonds : angle 3.98424 ( 1608) covalent geometry : bond 0.00240 (10959) covalent geometry : angle 0.47759 (14938) *********************** 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 144 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.198 Fit side-chains REVERT: C 231 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7578 (mp0) REVERT: C 402 THR cc_start: 0.6412 (m) cc_final: 0.5648 (t) REVERT: C 440 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: C 487 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 182 PHE cc_start: 0.7837 (m-80) cc_final: 0.7522 (m-10) REVERT: D 202 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7345 (t) REVERT: D 262 PHE cc_start: 0.6132 (p90) cc_final: 0.5794 (p90) REVERT: D 399 ASP cc_start: 0.7266 (m-30) cc_final: 0.6936 (t0) REVERT: D 518 MET cc_start: 0.8818 (mtt) cc_final: 0.8473 (mtt) REVERT: D 581 GLU cc_start: 0.8115 (tt0) cc_final: 0.7849 (tt0) REVERT: D 596 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7204 (mtp180) REVERT: D 624 GLN cc_start: 0.7549 (mp10) cc_final: 0.7282 (mp10) REVERT: D 758 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8200 (mm-30) outliers start: 23 outliers final: 5 residues processed: 140 average time/residue: 1.7562 time to fit residues: 262.3572 Evaluate side-chains 121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 440 GLU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 596 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 0.0470 chunk 6 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 5 optimal weight: 0.0040 chunk 49 optimal weight: 0.7980 overall best weight: 0.4490 ------------------------------------------------------------------------------- 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 37 HIS D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121837 restraints weight = 14075.700| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.79 r_work: 0.3347 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 10959 Z= 0.108 Angle : 0.476 6.264 14938 Z= 0.258 Chirality : 0.040 0.156 1675 Planarity : 0.004 0.055 1846 Dihedral : 14.146 178.419 1780 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.15 % Allowed : 16.99 % Favored : 80.86 % 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: 1.40 (0.24), residues: 1267 helix: 2.61 (0.21), residues: 600 sheet: -0.19 (0.37), residues: 199 loop : -0.82 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 PHE 0.014 0.001 PHE D 243 TYR 0.008 0.001 TYR D 145 ARG 0.011 0.000 ARG C 6 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 566) hydrogen bonds : angle 3.92854 ( 1608) covalent geometry : bond 0.00243 (10959) covalent geometry : angle 0.47587 (14938) *********************** 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 143 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.238 Fit side-chains REVERT: C 231 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7573 (mp0) REVERT: C 402 THR cc_start: 0.6315 (m) cc_final: 0.5584 (t) REVERT: C 425 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: C 440 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: D 202 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7349 (t) REVERT: D 262 PHE cc_start: 0.6057 (p90) cc_final: 0.5847 (p90) REVERT: D 399 ASP cc_start: 0.7270 (m-30) cc_final: 0.6966 (t0) REVERT: D 518 MET cc_start: 0.8817 (mtt) cc_final: 0.8495 (mtt) REVERT: D 581 GLU cc_start: 0.8118 (tt0) cc_final: 0.7844 (tt0) REVERT: D 596 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7195 (mtp180) REVERT: D 624 GLN cc_start: 0.7533 (mp10) cc_final: 0.7262 (mp10) REVERT: D 758 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8189 (mm-30) outliers start: 23 outliers final: 10 residues processed: 139 average time/residue: 1.5843 time to fit residues: 235.1862 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 425 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU 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 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 723 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 79 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 37 HIS D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118461 restraints weight = 13887.339| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.78 r_work: 0.3297 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10959 Z= 0.145 Angle : 0.510 6.890 14938 Z= 0.276 Chirality : 0.041 0.167 1675 Planarity : 0.004 0.056 1846 Dihedral : 14.306 176.746 1780 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 17.27 % Favored : 80.77 % 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: 1.31 (0.24), residues: 1267 helix: 2.48 (0.21), residues: 601 sheet: -0.18 (0.37), residues: 199 loop : -0.82 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 415 HIS 0.007 0.001 HIS D 281 PHE 0.015 0.001 PHE D 243 TYR 0.010 0.001 TYR C 63 ARG 0.010 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 566) hydrogen bonds : angle 4.09518 ( 1608) covalent geometry : bond 0.00342 (10959) covalent geometry : angle 0.50950 (14938) *********************** 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 145 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.322 Fit side-chains REVERT: C 163 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 231 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7571 (mp0) REVERT: C 402 THR cc_start: 0.6506 (m) cc_final: 0.5763 (t) REVERT: C 440 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7102 (pt0) REVERT: D 202 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7333 (t) REVERT: D 399 ASP cc_start: 0.7295 (m-30) cc_final: 0.6932 (t0) REVERT: D 581 GLU cc_start: 0.8154 (tt0) cc_final: 0.7838 (tt0) REVERT: D 596 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7173 (mtp180) REVERT: D 624 GLN cc_start: 0.7529 (mp10) cc_final: 0.7243 (mp10) REVERT: D 704 ASP cc_start: 0.7835 (p0) cc_final: 0.7470 (p0) REVERT: D 758 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 1.3657 time to fit residues: 208.1754 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR 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 290 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU 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 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 596 ARG 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 4 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 0.0980 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 37 HIS ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 232 ASN D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120448 restraints weight = 14053.436| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.79 r_work: 0.3325 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10959 Z= 0.118 Angle : 0.514 12.375 14938 Z= 0.273 Chirality : 0.040 0.177 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.188 177.769 1780 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.87 % Allowed : 17.37 % Favored : 80.77 % 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: 1.35 (0.24), residues: 1267 helix: 2.50 (0.21), residues: 600 sheet: -0.09 (0.37), residues: 199 loop : -0.81 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 415 HIS 0.004 0.001 HIS D 281 PHE 0.015 0.001 PHE D 243 TYR 0.008 0.001 TYR D 184 ARG 0.013 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 566) hydrogen bonds : angle 4.06739 ( 1608) covalent geometry : bond 0.00273 (10959) covalent geometry : angle 0.51414 (14938) *********************** 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 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.315 Fit side-chains REVERT: C 231 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7601 (mp0) REVERT: C 402 THR cc_start: 0.6347 (m) cc_final: 0.5638 (t) REVERT: C 440 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7102 (pt0) REVERT: D 184 TYR cc_start: 0.7341 (t80) cc_final: 0.7128 (t80) REVERT: D 202 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7329 (t) REVERT: D 262 PHE cc_start: 0.6064 (p90) cc_final: 0.5686 (p90) REVERT: D 399 ASP cc_start: 0.7294 (m-30) cc_final: 0.6959 (t0) REVERT: D 581 GLU cc_start: 0.8146 (tt0) cc_final: 0.7849 (tt0) REVERT: D 624 GLN cc_start: 0.7541 (mp10) cc_final: 0.7258 (mp10) REVERT: D 704 ASP cc_start: 0.7762 (p0) cc_final: 0.7445 (p0) REVERT: D 758 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8209 (mm-30) outliers start: 20 outliers final: 8 residues processed: 137 average time/residue: 1.6936 time to fit residues: 249.3085 Evaluate side-chains 128 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 440 GLU 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 444 LEU Chi-restraints excluded: chain D residue 523 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 0.0060 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 37 HIS ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117514 restraints weight = 13958.919| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.77 r_work: 0.3281 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10959 Z= 0.160 Angle : 0.551 11.807 14938 Z= 0.291 Chirality : 0.042 0.185 1675 Planarity : 0.004 0.058 1846 Dihedral : 14.400 176.170 1780 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.03 % Allowed : 18.67 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1267 helix: 2.36 (0.21), residues: 601 sheet: -0.13 (0.37), residues: 199 loop : -0.85 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 415 HIS 0.007 0.001 HIS D 281 PHE 0.016 0.001 PHE D 243 TYR 0.012 0.001 TYR C 63 ARG 0.013 0.001 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 566) hydrogen bonds : angle 4.24408 ( 1608) covalent geometry : bond 0.00382 (10959) covalent geometry : angle 0.55118 (14938) ********************** 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 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.128 Fit side-chains REVERT: C 113 ASP cc_start: 0.8136 (t70) cc_final: 0.7870 (t0) REVERT: C 231 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7637 (mp0) REVERT: C 401 PRO cc_start: 0.8113 (Cg_endo) cc_final: 0.7750 (Cg_exo) REVERT: C 402 THR cc_start: 0.6492 (m) cc_final: 0.5622 (t) REVERT: C 440 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: D 184 TYR cc_start: 0.7385 (t80) cc_final: 0.7176 (t80) REVERT: D 202 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7351 (t) REVERT: D 399 ASP cc_start: 0.7384 (m-30) cc_final: 0.6942 (t0) REVERT: D 581 GLU cc_start: 0.8149 (tt0) cc_final: 0.7842 (tt0) REVERT: D 624 GLN cc_start: 0.7493 (mp10) cc_final: 0.7203 (mp10) REVERT: D 704 ASP cc_start: 0.7710 (p0) cc_final: 0.7390 (p0) REVERT: D 758 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8267 (mm-30) outliers start: 11 outliers final: 7 residues processed: 128 average time/residue: 1.4919 time to fit residues: 203.8749 Evaluate side-chains 121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 440 GLU 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 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 37 HIS ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118568 restraints weight = 13891.128| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.77 r_work: 0.3296 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10959 Z= 0.134 Angle : 0.540 11.687 14938 Z= 0.284 Chirality : 0.041 0.183 1675 Planarity : 0.004 0.059 1846 Dihedral : 14.326 176.715 1780 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.12 % Allowed : 18.86 % Favored : 80.02 % 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: 1.21 (0.24), residues: 1267 helix: 2.35 (0.21), residues: 601 sheet: -0.11 (0.37), residues: 199 loop : -0.86 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 415 HIS 0.005 0.001 HIS D 281 PHE 0.015 0.001 PHE D 243 TYR 0.009 0.001 TYR D 145 ARG 0.014 0.000 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 566) hydrogen bonds : angle 4.21443 ( 1608) covalent geometry : bond 0.00315 (10959) covalent geometry : angle 0.54046 (14938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9182.91 seconds wall clock time: 163 minutes 51.84 seconds (9831.84 seconds total)