Starting phenix.real_space_refine on Mon Jul 28 13:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oma_70610/07_2025/9oma_70610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oma_70610/07_2025/9oma_70610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oma_70610/07_2025/9oma_70610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oma_70610/07_2025/9oma_70610.map" model { file = "/net/cci-nas-00/data/ceres_data/9oma_70610/07_2025/9oma_70610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oma_70610/07_2025/9oma_70610.cif" } resolution = 4.14 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= -0.022 sd= 0.230 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6575 2.51 5 N 1760 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 10325 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2232 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain breaks: 1 Chain: "B" Number of atoms: 5959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5959 Classifications: {'peptide': 723} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 701} Chain breaks: 3 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 680 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 1 Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 7.83, per 1000 atoms: 0.76 Number of scatterers: 10325 At special positions: 0 Unit cell: (90.3, 110.08, 191.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1920 8.00 N 1760 7.00 C 6575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 73 " distance=2.03 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 56.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.789A pdb=" N TYR A 51 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.541A pdb=" N ILE A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.535A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.837A pdb=" N ILE A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'B' and resid 21 through 31 removed outlier: 3.729A pdb=" N ARG B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 removed outlier: 4.071A pdb=" N PHE B 44 " --> pdb=" O TRP B 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 82 Processing helix chain 'B' and resid 85 through 105 removed outlier: 4.174A pdb=" N ASP B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 147 through 168 removed outlier: 3.645A pdb=" N ILE B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 160 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 removed outlier: 4.584A pdb=" N VAL B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 202 through 218 Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.050A pdb=" N GLN B 223 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 289 through 301 removed outlier: 4.206A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 333 removed outlier: 4.392A pdb=" N ASP B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 359 removed outlier: 3.635A pdb=" N TYR B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 378 Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.510A pdb=" N ASN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'B' and resid 426 through 442 removed outlier: 3.587A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 removed outlier: 3.685A pdb=" N ARG B 452 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 484 removed outlier: 3.538A pdb=" N MET B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 491 through 514 removed outlier: 3.524A pdb=" N MET B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 597 through 608 removed outlier: 4.017A pdb=" N GLN B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 626 through 639 Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 689 through 694 removed outlier: 3.803A pdb=" N GLN B 693 " --> pdb=" O GLY B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 726 removed outlier: 4.087A pdb=" N ARG B 700 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 742 removed outlier: 3.934A pdb=" N GLU B 740 " --> pdb=" O THR B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 749 through 763 removed outlier: 4.370A pdb=" N GLU B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.602A pdb=" N GLU C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.775A pdb=" N LEU D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 23 through 29 Processing helix chain 'E' and resid 50 through 68 removed outlier: 3.671A pdb=" N LYS E 56 " --> pdb=" O HIS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.821A pdb=" N ASN E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 147 removed outlier: 7.161A pdb=" N SER A 83 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP A 161 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 188 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 163 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N CYS A 165 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 185 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 200 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 195 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 531 through 532 removed outlier: 6.223A pdb=" N LEU B 531 " --> pdb=" O TRP C 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 579 through 585 Processing sheet with id=AA5, first strand: chain 'B' and resid 614 through 615 Processing sheet with id=AA6, first strand: chain 'B' and resid 675 through 676 Processing sheet with id=AA7, first strand: chain 'B' and resid 728 through 730 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77 Processing sheet with id=AA9, first strand: chain 'D' and resid 73 through 75 removed outlier: 3.777A pdb=" N ARG D 8 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 15 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS E 16 " --> pdb=" O PHE D 15 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3383 1.34 - 1.46: 2207 1.46 - 1.58: 4819 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10520 Sorted by residual: bond pdb=" N THR B 695 " pdb=" CA THR B 695 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N ILE B 766 " pdb=" CA ILE B 766 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N ILE B 147 " pdb=" CA ILE B 147 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.21e-02 6.83e+03 8.51e+00 bond pdb=" N VAL B 619 " pdb=" CA VAL B 619 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.14e+00 ... (remaining 10515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 13748 1.92 - 3.85: 397 3.85 - 5.77: 39 5.77 - 7.69: 1 7.69 - 9.61: 1 Bond angle restraints: 14186 Sorted by residual: angle pdb=" CA THR B 696 " pdb=" C THR B 696 " pdb=" O THR B 696 " ideal model delta sigma weight residual 121.60 116.81 4.79 1.21e+00 6.83e-01 1.57e+01 angle pdb=" CA GLU B 259 " pdb=" C GLU B 259 " pdb=" O GLU B 259 " ideal model delta sigma weight residual 120.55 116.51 4.04 1.06e+00 8.90e-01 1.45e+01 angle pdb=" CA THR B 696 " pdb=" CB THR B 696 " pdb=" OG1 THR B 696 " ideal model delta sigma weight residual 109.60 104.46 5.14 1.50e+00 4.44e-01 1.17e+01 angle pdb=" CA THR B 695 " pdb=" C THR B 695 " pdb=" O THR B 695 " ideal model delta sigma weight residual 121.45 117.90 3.55 1.07e+00 8.73e-01 1.10e+01 angle pdb=" CA VAL B 258 " pdb=" C VAL B 258 " pdb=" O VAL B 258 " ideal model delta sigma weight residual 121.17 117.69 3.48 1.06e+00 8.90e-01 1.08e+01 ... (remaining 14181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 5836 16.33 - 32.66: 447 32.66 - 48.99: 131 48.99 - 65.32: 39 65.32 - 81.65: 18 Dihedral angle restraints: 6471 sinusoidal: 2723 harmonic: 3748 Sorted by residual: dihedral pdb=" CA LEU B 107 " pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 50 " pdb=" SG CYS C 50 " pdb=" SG CYS C 53 " pdb=" CB CYS C 53 " ideal model delta sinusoidal sigma weight residual 93.00 133.81 -40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CA PRO D 72 " pdb=" C PRO D 72 " pdb=" N ALA D 73 " pdb=" CA ALA D 73 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1151 0.040 - 0.081: 297 0.081 - 0.121: 102 0.121 - 0.161: 18 0.161 - 0.202: 7 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA ILE B 766 " pdb=" N ILE B 766 " pdb=" C ILE B 766 " pdb=" CB ILE B 766 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU B 694 " pdb=" N LEU B 694 " pdb=" C LEU B 694 " pdb=" CB LEU B 694 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA VAL B 619 " pdb=" N VAL B 619 " pdb=" C VAL B 619 " pdb=" CB VAL B 619 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 1572 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 43 " 0.270 9.50e-02 1.11e+02 1.21e-01 8.96e+00 pdb=" NE ARG D 43 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 43 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 43 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 43 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO B 108 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 65 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 66 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.028 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2905 2.81 - 3.34: 10492 3.34 - 3.86: 16801 3.86 - 4.38: 20026 4.38 - 4.90: 32841 Nonbonded interactions: 83065 Sorted by model distance: nonbonded pdb=" N TYR D 45 " pdb=" O LEU D 77 " model vdw 2.293 3.120 nonbonded pdb=" O GLY E 32 " pdb=" O PRO E 33 " model vdw 2.334 3.040 nonbonded pdb=" O ARG D 68 " pdb=" O ALA D 71 " model vdw 2.344 3.040 nonbonded pdb=" O GLY A 228 " pdb=" OG SER A 232 " model vdw 2.358 3.040 nonbonded pdb=" O ILE E 26 " pdb=" O MET E 29 " model vdw 2.403 3.040 ... (remaining 83060 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.270 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10522 Z= 0.292 Angle : 0.733 9.614 14190 Z= 0.444 Chirality : 0.044 0.202 1575 Planarity : 0.006 0.121 1818 Dihedral : 14.120 81.655 4015 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.46 % Favored : 94.14 % Rotamer: Outliers : 2.01 % Allowed : 8.55 % Favored : 89.44 % 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: -0.64 (0.24), residues: 1246 helix: 0.26 (0.21), residues: 618 sheet: -0.21 (0.63), residues: 59 loop : -1.17 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 97 HIS 0.010 0.002 HIS A 173 PHE 0.034 0.002 PHE E 13 TYR 0.017 0.002 TYR A 160 ARG 0.007 0.001 ARG E 17 Details of bonding type rmsd hydrogen bonds : bond 0.16183 ( 510) hydrogen bonds : angle 7.09491 ( 1470) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.46611 ( 4) covalent geometry : bond 0.00533 (10520) covalent geometry : angle 0.73310 (14186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 ASN cc_start: 0.6910 (OUTLIER) cc_final: 0.6587 (t0) REVERT: B 188 CYS cc_start: 0.7768 (m) cc_final: 0.7383 (m) REVERT: B 249 LEU cc_start: 0.6761 (mt) cc_final: 0.6550 (mt) REVERT: B 292 LYS cc_start: 0.7857 (mttt) cc_final: 0.7628 (mttp) REVERT: B 492 LYS cc_start: 0.9034 (tttm) cc_final: 0.8798 (tptt) REVERT: B 672 PHE cc_start: 0.7863 (t80) cc_final: 0.7017 (t80) REVERT: B 682 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7611 (tptt) REVERT: B 762 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 41 GLU cc_start: 0.3384 (OUTLIER) cc_final: 0.2108 (mt-10) REVERT: E 11 HIS cc_start: 0.7038 (t70) cc_final: 0.6526 (t-90) REVERT: E 59 MET cc_start: 0.7415 (ttp) cc_final: 0.7143 (ttm) outliers start: 23 outliers final: 4 residues processed: 282 average time/residue: 0.2805 time to fit residues: 104.6541 Evaluate side-chains 184 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.0050 overall best weight: 0.7214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 32 GLN B 103 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 288 ASN B 475 ASN B 599 GLN C 82 HIS ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.110892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.093057 restraints weight = 58995.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.094602 restraints weight = 36740.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.095811 restraints weight = 25856.018| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10522 Z= 0.176 Angle : 0.695 8.718 14190 Z= 0.361 Chirality : 0.044 0.197 1575 Planarity : 0.006 0.066 1818 Dihedral : 4.761 23.900 1366 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -0.37 (0.23), residues: 1246 helix: 0.64 (0.21), residues: 623 sheet: 0.67 (0.66), residues: 54 loop : -1.33 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 759 HIS 0.011 0.001 HIS A 62 PHE 0.021 0.002 PHE B 365 TYR 0.021 0.002 TYR B 233 ARG 0.008 0.001 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.05698 ( 510) hydrogen bonds : angle 5.29540 ( 1470) SS BOND : bond 0.00086 ( 2) SS BOND : angle 0.56545 ( 4) covalent geometry : bond 0.00393 (10520) covalent geometry : angle 0.69468 (14186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.6920 (p0) cc_final: 0.6712 (p0) REVERT: A 173 HIS cc_start: 0.6847 (m90) cc_final: 0.6334 (m-70) REVERT: B 188 CYS cc_start: 0.8048 (m) cc_final: 0.7426 (p) REVERT: B 292 LYS cc_start: 0.8727 (mttt) cc_final: 0.8507 (mttp) REVERT: B 474 GLU cc_start: 0.8048 (mp0) cc_final: 0.7435 (tp30) REVERT: B 629 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8544 (mt-10) REVERT: B 640 PHE cc_start: 0.7961 (t80) cc_final: 0.7623 (t80) REVERT: B 660 PHE cc_start: 0.7335 (m-80) cc_final: 0.6395 (m-10) REVERT: B 682 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7808 (tptt) REVERT: B 694 LEU cc_start: 0.8199 (mt) cc_final: 0.7833 (tp) REVERT: C 35 TRP cc_start: 0.2899 (t60) cc_final: 0.1744 (t60) REVERT: D 31 VAL cc_start: 0.8171 (p) cc_final: 0.7930 (m) REVERT: E 11 HIS cc_start: 0.6545 (t70) cc_final: 0.6218 (t70) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2773 time to fit residues: 82.1740 Evaluate side-chains 166 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 62 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: A 194 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** 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 = 0.4216 r_free = 0.4216 target = 0.108960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.090950 restraints weight = 58754.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.092471 restraints weight = 36767.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.093615 restraints weight = 26061.578| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10522 Z= 0.160 Angle : 0.651 8.349 14190 Z= 0.339 Chirality : 0.043 0.172 1575 Planarity : 0.005 0.077 1818 Dihedral : 4.691 30.546 1366 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % 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: -0.45 (0.23), residues: 1246 helix: 0.57 (0.20), residues: 639 sheet: 0.46 (0.60), residues: 64 loop : -1.44 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 759 HIS 0.008 0.001 HIS B 457 PHE 0.031 0.002 PHE A 33 TYR 0.019 0.002 TYR B 562 ARG 0.005 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 510) hydrogen bonds : angle 5.03000 ( 1470) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.43893 ( 4) covalent geometry : bond 0.00353 (10520) covalent geometry : angle 0.65096 (14186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.6991 (m90) cc_final: 0.6638 (m-70) REVERT: A 339 MET cc_start: 0.7710 (mmm) cc_final: 0.7308 (mtp) REVERT: B 188 CYS cc_start: 0.8009 (m) cc_final: 0.7358 (p) REVERT: B 231 MET cc_start: 0.6716 (mtm) cc_final: 0.6230 (mtm) REVERT: B 252 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7435 (ttm110) REVERT: B 629 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8569 (mt-10) REVERT: B 630 LEU cc_start: 0.8445 (mt) cc_final: 0.8243 (mt) REVERT: B 631 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7886 (mtt-85) REVERT: B 660 PHE cc_start: 0.7315 (m-80) cc_final: 0.6383 (m-10) REVERT: B 670 GLN cc_start: 0.7005 (mp10) cc_final: 0.6651 (tp-100) REVERT: B 682 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7787 (tptt) REVERT: B 694 LEU cc_start: 0.8256 (mt) cc_final: 0.7872 (tp) REVERT: B 743 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7899 (ptpt) REVERT: B 751 LYS cc_start: 0.8849 (pttm) cc_final: 0.8396 (pttm) REVERT: C 35 TRP cc_start: 0.2977 (t60) cc_final: 0.1758 (t60) REVERT: D 31 VAL cc_start: 0.8177 (p) cc_final: 0.7892 (m) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.2786 time to fit residues: 78.7130 Evaluate side-chains 176 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 175 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.108316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.092301 restraints weight = 59132.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.092154 restraints weight = 45154.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.093127 restraints weight = 32861.613| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10522 Z= 0.162 Angle : 0.662 8.229 14190 Z= 0.340 Chirality : 0.043 0.176 1575 Planarity : 0.005 0.105 1818 Dihedral : 4.806 35.301 1366 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.51 (0.24), residues: 1246 helix: 0.50 (0.20), residues: 639 sheet: 0.43 (0.60), residues: 64 loop : -1.44 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 759 HIS 0.008 0.001 HIS B 457 PHE 0.020 0.002 PHE B 273 TYR 0.018 0.002 TYR E 63 ARG 0.010 0.001 ARG B 452 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 510) hydrogen bonds : angle 4.99560 ( 1470) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.56806 ( 4) covalent geometry : bond 0.00358 (10520) covalent geometry : angle 0.66187 (14186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8080 (mp) cc_final: 0.7777 (mp) REVERT: A 173 HIS cc_start: 0.6938 (m90) cc_final: 0.6531 (m-70) REVERT: B 188 CYS cc_start: 0.7871 (m) cc_final: 0.7330 (p) REVERT: B 360 GLN cc_start: 0.9216 (mm110) cc_final: 0.8533 (mm110) REVERT: B 629 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8525 (mt-10) REVERT: B 630 LEU cc_start: 0.8349 (mt) cc_final: 0.8006 (mt) REVERT: B 660 PHE cc_start: 0.7482 (m-80) cc_final: 0.6562 (m-10) REVERT: B 743 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8017 (ptpt) REVERT: C 35 TRP cc_start: 0.2685 (t60) cc_final: 0.1821 (t60) REVERT: D 90 ILE cc_start: 0.7223 (mt) cc_final: 0.6944 (pt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2731 time to fit residues: 74.2636 Evaluate side-chains 166 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.0170 chunk 83 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 586 ASN C 109 GLN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.108509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.090730 restraints weight = 59299.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.092175 restraints weight = 36723.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.093322 restraints weight = 26062.185| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10522 Z= 0.133 Angle : 0.609 7.776 14190 Z= 0.314 Chirality : 0.043 0.334 1575 Planarity : 0.005 0.075 1818 Dihedral : 4.680 37.112 1366 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 0.09 % Allowed : 1.92 % Favored : 97.99 % 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: -0.48 (0.24), residues: 1246 helix: 0.46 (0.20), residues: 643 sheet: 0.73 (0.63), residues: 64 loop : -1.39 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 759 HIS 0.005 0.001 HIS B 457 PHE 0.029 0.002 PHE A 33 TYR 0.014 0.002 TYR E 63 ARG 0.007 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 510) hydrogen bonds : angle 4.89135 ( 1470) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.56435 ( 4) covalent geometry : bond 0.00295 (10520) covalent geometry : angle 0.60867 (14186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7126 (tp-100) cc_final: 0.6804 (tp-100) REVERT: A 173 HIS cc_start: 0.6713 (m90) cc_final: 0.6357 (m-70) REVERT: A 204 ASN cc_start: 0.8368 (p0) cc_final: 0.7950 (m-40) REVERT: B 188 CYS cc_start: 0.7866 (m) cc_final: 0.7307 (p) REVERT: B 591 TYR cc_start: 0.5764 (p90) cc_final: 0.5541 (p90) REVERT: B 629 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8616 (mt-10) REVERT: B 630 LEU cc_start: 0.8433 (mt) cc_final: 0.8146 (mt) REVERT: B 640 PHE cc_start: 0.8202 (t80) cc_final: 0.7819 (t80) REVERT: B 660 PHE cc_start: 0.7470 (m-80) cc_final: 0.6517 (m-10) REVERT: B 672 PHE cc_start: 0.7779 (t80) cc_final: 0.7423 (t80) REVERT: B 743 LYS cc_start: 0.8300 (ptpp) cc_final: 0.8055 (ptpt) REVERT: C 29 MET cc_start: 0.4831 (ttp) cc_final: 0.4631 (ttp) REVERT: D 90 ILE cc_start: 0.6957 (mt) cc_final: 0.6722 (pt) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2756 time to fit residues: 72.8860 Evaluate side-chains 169 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.0470 chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS B 572 HIS C 109 GLN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.108511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.092576 restraints weight = 58383.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.092734 restraints weight = 44543.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.093418 restraints weight = 32300.029| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10522 Z= 0.133 Angle : 0.628 9.134 14190 Z= 0.323 Chirality : 0.043 0.301 1575 Planarity : 0.005 0.073 1818 Dihedral : 4.684 38.955 1366 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1246 helix: 0.44 (0.20), residues: 640 sheet: 0.66 (0.62), residues: 64 loop : -1.39 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 56 HIS 0.004 0.001 HIS B 457 PHE 0.020 0.001 PHE B 273 TYR 0.024 0.002 TYR A 69 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 510) hydrogen bonds : angle 4.85503 ( 1470) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.53137 ( 4) covalent geometry : bond 0.00290 (10520) covalent geometry : angle 0.62780 (14186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7620 (p0) cc_final: 0.7318 (p0) REVERT: A 173 HIS cc_start: 0.7113 (m-70) cc_final: 0.6600 (m-70) REVERT: A 204 ASN cc_start: 0.8447 (p0) cc_final: 0.8101 (m-40) REVERT: A 339 MET cc_start: 0.7674 (mmm) cc_final: 0.7454 (mmm) REVERT: B 188 CYS cc_start: 0.7880 (m) cc_final: 0.7333 (p) REVERT: B 629 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8585 (mt-10) REVERT: B 630 LEU cc_start: 0.8404 (mt) cc_final: 0.8123 (mt) REVERT: B 640 PHE cc_start: 0.7863 (t80) cc_final: 0.7409 (t80) REVERT: B 660 PHE cc_start: 0.7457 (m-80) cc_final: 0.6583 (m-10) REVERT: B 699 MET cc_start: 0.7735 (ttt) cc_final: 0.7259 (ttt) REVERT: B 743 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8138 (ptpt) REVERT: B 752 MET cc_start: 0.8992 (pmm) cc_final: 0.8561 (pmm) REVERT: B 775 THR cc_start: 0.9320 (m) cc_final: 0.8798 (m) REVERT: D 90 ILE cc_start: 0.7252 (mt) cc_final: 0.6937 (pt) REVERT: E 59 MET cc_start: 0.6832 (tmm) cc_final: 0.6578 (mmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3218 time to fit residues: 82.9393 Evaluate side-chains 165 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 586 ASN B 756 GLN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.107119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.091187 restraints weight = 59181.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091288 restraints weight = 41159.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.092070 restraints weight = 29166.410| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10522 Z= 0.157 Angle : 0.655 9.596 14190 Z= 0.338 Chirality : 0.044 0.283 1575 Planarity : 0.006 0.182 1818 Dihedral : 4.818 39.252 1366 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.62 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.68 (0.24), residues: 1246 helix: 0.29 (0.20), residues: 651 sheet: 0.60 (0.62), residues: 64 loop : -1.49 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.007 0.001 HIS B 457 PHE 0.022 0.002 PHE B 273 TYR 0.018 0.002 TYR E 63 ARG 0.004 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 510) hydrogen bonds : angle 4.90477 ( 1470) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.49446 ( 4) covalent geometry : bond 0.00355 (10520) covalent geometry : angle 0.65470 (14186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7700 (p0) cc_final: 0.7372 (p0) REVERT: A 173 HIS cc_start: 0.7082 (m-70) cc_final: 0.6541 (m-70) REVERT: A 204 ASN cc_start: 0.8440 (p0) cc_final: 0.8120 (m-40) REVERT: A 212 LEU cc_start: 0.8986 (mm) cc_final: 0.8635 (mt) REVERT: A 339 MET cc_start: 0.7808 (mmm) cc_final: 0.7553 (mmm) REVERT: B 591 TYR cc_start: 0.5644 (p90) cc_final: 0.5197 (p90) REVERT: B 629 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8579 (mt-10) REVERT: B 630 LEU cc_start: 0.8457 (mt) cc_final: 0.8247 (mt) REVERT: B 640 PHE cc_start: 0.7989 (t80) cc_final: 0.7487 (t80) REVERT: B 660 PHE cc_start: 0.7572 (m-80) cc_final: 0.6656 (m-10) REVERT: B 672 PHE cc_start: 0.7559 (t80) cc_final: 0.7187 (t80) REVERT: B 699 MET cc_start: 0.7713 (ttt) cc_final: 0.7250 (ttt) REVERT: B 743 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8170 (ptpt) REVERT: B 779 MET cc_start: 0.4725 (mpp) cc_final: 0.4500 (mmt) REVERT: C 29 MET cc_start: 0.4565 (ttp) cc_final: 0.4361 (ttp) REVERT: C 40 MET cc_start: 0.6368 (tmm) cc_final: 0.5964 (tmm) REVERT: D 90 ILE cc_start: 0.7256 (mt) cc_final: 0.6919 (pt) REVERT: E 59 MET cc_start: 0.7036 (tmm) cc_final: 0.6504 (mmt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2738 time to fit residues: 70.1836 Evaluate side-chains 164 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** 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 = 0.4179 r_free = 0.4179 target = 0.104452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.089798 restraints weight = 61584.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.091291 restraints weight = 37630.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092407 restraints weight = 26086.315| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10522 Z= 0.135 Angle : 0.660 8.797 14190 Z= 0.337 Chirality : 0.044 0.304 1575 Planarity : 0.005 0.073 1818 Dihedral : 4.768 39.366 1366 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1246 helix: 0.32 (0.20), residues: 654 sheet: 0.77 (0.62), residues: 62 loop : -1.54 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 35 HIS 0.005 0.001 HIS A 173 PHE 0.018 0.002 PHE B 273 TYR 0.016 0.002 TYR D 45 ARG 0.013 0.000 ARG B 452 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 510) hydrogen bonds : angle 4.83868 ( 1470) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.81264 ( 4) covalent geometry : bond 0.00294 (10520) covalent geometry : angle 0.65948 (14186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7764 (p0) cc_final: 0.7455 (p0) REVERT: A 173 HIS cc_start: 0.7219 (m-70) cc_final: 0.6621 (m-70) REVERT: A 204 ASN cc_start: 0.8530 (p0) cc_final: 0.8225 (m-40) REVERT: A 212 LEU cc_start: 0.8904 (mm) cc_final: 0.8592 (mt) REVERT: A 339 MET cc_start: 0.7808 (mmm) cc_final: 0.7584 (mmm) REVERT: B 591 TYR cc_start: 0.5526 (p90) cc_final: 0.5323 (p90) REVERT: B 630 LEU cc_start: 0.8428 (mt) cc_final: 0.8091 (mt) REVERT: B 640 PHE cc_start: 0.7833 (t80) cc_final: 0.7362 (t80) REVERT: B 660 PHE cc_start: 0.7465 (m-80) cc_final: 0.6629 (m-10) REVERT: B 672 PHE cc_start: 0.7059 (t80) cc_final: 0.6850 (t80) REVERT: B 699 MET cc_start: 0.7284 (ttt) cc_final: 0.6952 (ttt) REVERT: B 743 LYS cc_start: 0.8407 (ptpp) cc_final: 0.8155 (ptpt) REVERT: B 752 MET cc_start: 0.8716 (pmm) cc_final: 0.8463 (pmm) REVERT: B 772 ASP cc_start: 0.7987 (t70) cc_final: 0.7684 (t70) REVERT: B 775 THR cc_start: 0.9002 (m) cc_final: 0.8183 (p) REVERT: B 779 MET cc_start: 0.4092 (mpp) cc_final: 0.3746 (mmt) REVERT: C 40 MET cc_start: 0.6940 (tmm) cc_final: 0.6561 (tmm) REVERT: C 89 MET cc_start: 0.7373 (pmm) cc_final: 0.7134 (pmm) REVERT: D 90 ILE cc_start: 0.7013 (mt) cc_final: 0.6805 (pt) REVERT: E 6 ILE cc_start: 0.7990 (mp) cc_final: 0.7762 (mt) REVERT: E 59 MET cc_start: 0.6877 (tmm) cc_final: 0.6612 (mmt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.3130 time to fit residues: 78.3612 Evaluate side-chains 162 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN C 109 GLN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.107930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.090180 restraints weight = 60257.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.091625 restraints weight = 37144.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.092752 restraints weight = 26471.301| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10522 Z= 0.133 Angle : 0.652 9.642 14190 Z= 0.337 Chirality : 0.045 0.370 1575 Planarity : 0.004 0.072 1818 Dihedral : 4.781 39.388 1366 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.62 (0.24), residues: 1246 helix: 0.38 (0.20), residues: 650 sheet: 0.78 (0.63), residues: 62 loop : -1.54 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 35 HIS 0.034 0.002 HIS B 763 PHE 0.018 0.002 PHE B 273 TYR 0.018 0.002 TYR D 45 ARG 0.008 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 510) hydrogen bonds : angle 4.82438 ( 1470) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.73514 ( 4) covalent geometry : bond 0.00291 (10520) covalent geometry : angle 0.65226 (14186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7617 (p0) cc_final: 0.7240 (p0) REVERT: A 173 HIS cc_start: 0.6949 (m-70) cc_final: 0.6394 (m-70) REVERT: A 196 THR cc_start: 0.6694 (p) cc_final: 0.5335 (p) REVERT: A 204 ASN cc_start: 0.8367 (p0) cc_final: 0.8114 (m-40) REVERT: A 212 LEU cc_start: 0.8918 (mm) cc_final: 0.8608 (mt) REVERT: A 339 MET cc_start: 0.7771 (mmm) cc_final: 0.7538 (mmm) REVERT: B 231 MET cc_start: 0.6433 (mtp) cc_final: 0.6165 (mtm) REVERT: B 436 GLU cc_start: 0.7704 (tp30) cc_final: 0.7495 (mm-30) REVERT: B 629 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8700 (mt-10) REVERT: B 640 PHE cc_start: 0.8125 (t80) cc_final: 0.7770 (t80) REVERT: B 660 PHE cc_start: 0.7637 (m-80) cc_final: 0.6684 (m-10) REVERT: B 699 MET cc_start: 0.8025 (ttt) cc_final: 0.7483 (ttt) REVERT: B 754 LYS cc_start: 0.9517 (tmtt) cc_final: 0.9295 (tptp) REVERT: B 769 ASP cc_start: 0.8190 (t0) cc_final: 0.7882 (t0) REVERT: B 772 ASP cc_start: 0.8828 (t70) cc_final: 0.8521 (t70) REVERT: B 775 THR cc_start: 0.9245 (m) cc_final: 0.8744 (p) REVERT: B 779 MET cc_start: 0.5000 (mpp) cc_final: 0.4782 (mmt) REVERT: C 29 MET cc_start: 0.4696 (ttp) cc_final: 0.4460 (ttp) REVERT: C 40 MET cc_start: 0.6522 (tmm) cc_final: 0.6163 (tmm) REVERT: D 90 ILE cc_start: 0.7192 (mt) cc_final: 0.6818 (pt) REVERT: E 59 MET cc_start: 0.6831 (tmm) cc_final: 0.6330 (mmt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3625 time to fit residues: 90.3840 Evaluate side-chains 158 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.090009 restraints weight = 61726.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.091470 restraints weight = 37433.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092557 restraints weight = 25904.280| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10522 Z= 0.132 Angle : 0.656 10.252 14190 Z= 0.336 Chirality : 0.045 0.213 1575 Planarity : 0.005 0.072 1818 Dihedral : 4.789 39.391 1366 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.64 (0.24), residues: 1246 helix: 0.33 (0.20), residues: 664 sheet: 0.79 (0.64), residues: 62 loop : -1.54 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 143 HIS 0.023 0.001 HIS B 763 PHE 0.017 0.002 PHE D 4 TYR 0.020 0.002 TYR D 45 ARG 0.016 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 510) hydrogen bonds : angle 4.85805 ( 1470) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.69202 ( 4) covalent geometry : bond 0.00284 (10520) covalent geometry : angle 0.65638 (14186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7777 (p0) cc_final: 0.7405 (p0) REVERT: A 173 HIS cc_start: 0.7211 (m-70) cc_final: 0.6640 (m-70) REVERT: A 196 THR cc_start: 0.6637 (p) cc_final: 0.5283 (p) REVERT: A 204 ASN cc_start: 0.8554 (p0) cc_final: 0.8277 (m-40) REVERT: A 212 LEU cc_start: 0.8940 (mm) cc_final: 0.8647 (mt) REVERT: A 339 MET cc_start: 0.7779 (mmm) cc_final: 0.7505 (mmm) REVERT: B 252 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7788 (mtp85) REVERT: B 336 ASP cc_start: 0.7205 (t0) cc_final: 0.6733 (t0) REVERT: B 640 PHE cc_start: 0.7866 (t80) cc_final: 0.7411 (t80) REVERT: B 660 PHE cc_start: 0.7602 (m-80) cc_final: 0.6812 (m-10) REVERT: B 772 ASP cc_start: 0.8061 (t70) cc_final: 0.7842 (t70) REVERT: B 775 THR cc_start: 0.8968 (m) cc_final: 0.8197 (p) REVERT: B 779 MET cc_start: 0.4002 (mpp) cc_final: 0.3551 (mmt) REVERT: C 40 MET cc_start: 0.7128 (tmm) cc_final: 0.6871 (tmm) REVERT: D 90 ILE cc_start: 0.7159 (mt) cc_final: 0.6786 (pt) REVERT: E 59 MET cc_start: 0.6872 (tmm) cc_final: 0.6399 (mmm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3231 time to fit residues: 81.1054 Evaluate side-chains 160 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 774 ASN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.103110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.088891 restraints weight = 61236.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.090263 restraints weight = 37931.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.091258 restraints weight = 26355.483| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10522 Z= 0.160 Angle : 0.694 9.934 14190 Z= 0.359 Chirality : 0.045 0.182 1575 Planarity : 0.005 0.073 1818 Dihedral : 4.967 39.199 1366 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1246 helix: 0.29 (0.20), residues: 658 sheet: 0.75 (0.65), residues: 62 loop : -1.58 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 41 HIS 0.022 0.001 HIS B 763 PHE 0.021 0.002 PHE D 4 TYR 0.026 0.002 TYR D 45 ARG 0.014 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 510) hydrogen bonds : angle 4.96630 ( 1470) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.66930 ( 4) covalent geometry : bond 0.00356 (10520) covalent geometry : angle 0.69447 (14186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.51 seconds wall clock time: 86 minutes 9.09 seconds (5169.09 seconds total)