Starting phenix.real_space_refine on Wed Apr 30 16:48:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hd5_0201/04_2025/6hd5_0201_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hd5_0201/04_2025/6hd5_0201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hd5_0201/04_2025/6hd5_0201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hd5_0201/04_2025/6hd5_0201.map" model { file = "/net/cci-nas-00/data/ceres_data/6hd5_0201/04_2025/6hd5_0201_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hd5_0201/04_2025/6hd5_0201_neut.cif" } resolution = 4.8 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= 0.001 sd= 0.010 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 38 5.16 5 C 6209 2.51 5 N 1643 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9707 Number of models: 1 Model: "" Number of chains: 3 Chain: "t" Number of atoms: 6650 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 838, 6650 Classifications: {'peptide': 838} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 27, 'TRANS': 810} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "u" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1798 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 227} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "v" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1259 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PHE v 36 " occ=0.79 ... (9 atoms not shown) pdb=" CZ PHE v 36 " occ=0.79 Time building chain proxies: 6.32, per 1000 atoms: 0.65 Number of scatterers: 9707 At special positions: 0 Unit cell: (123.576, 110.568, 113.82, 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 38 16.00 O 1817 8.00 N 1643 7.00 C 6209 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 61.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 't' and resid 18 through 33 removed outlier: 3.564A pdb=" N ASP t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS t 29 " --> pdb=" O LEU t 25 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU t 30 " --> pdb=" O GLU t 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR t 31 " --> pdb=" O ALA t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 36 through 50 removed outlier: 3.768A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 68 removed outlier: 3.569A pdb=" N GLY t 68 " --> pdb=" O LEU t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 83 Processing helix chain 't' and resid 90 through 104 removed outlier: 3.722A pdb=" N CYS t 94 " --> pdb=" O SER t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 107 through 122 removed outlier: 3.587A pdb=" N GLY t 121 " --> pdb=" O ALA t 117 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER t 122 " --> pdb=" O LEU t 118 " (cutoff:3.500A) Processing helix chain 't' and resid 125 through 139 removed outlier: 3.771A pdb=" N ARG t 129 " --> pdb=" O LYS t 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER t 136 " --> pdb=" O ALA t 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE t 138 " --> pdb=" O LEU t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 141 through 155 removed outlier: 3.866A pdb=" N VAL t 146 " --> pdb=" O LYS t 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE t 155 " --> pdb=" O TYR t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 158 through 173 removed outlier: 3.966A pdb=" N TRP t 162 " --> pdb=" O TYR t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 174 through 189 Processing helix chain 't' and resid 195 through 215 removed outlier: 4.328A pdb=" N TYR t 199 " --> pdb=" O ASP t 195 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU t 200 " --> pdb=" O SER t 196 " (cutoff:3.500A) Processing helix chain 't' and resid 219 through 234 Processing helix chain 't' and resid 240 through 255 Processing helix chain 't' and resid 256 through 271 removed outlier: 3.764A pdb=" N ALA t 260 " --> pdb=" O GLN t 256 " (cutoff:3.500A) Processing helix chain 't' and resid 274 through 286 removed outlier: 3.579A pdb=" N TYR t 278 " --> pdb=" O ASN t 274 " (cutoff:3.500A) Processing helix chain 't' and resid 290 through 303 removed outlier: 3.989A pdb=" N LYS t 294 " --> pdb=" O ASP t 290 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN t 303 " --> pdb=" O GLY t 299 " (cutoff:3.500A) Processing helix chain 't' and resid 309 through 314 Processing helix chain 't' and resid 315 through 318 removed outlier: 3.904A pdb=" N PHE t 318 " --> pdb=" O PRO t 315 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 315 through 318' Processing helix chain 't' and resid 321 through 340 Proline residue: t 335 - end of helix Processing helix chain 't' and resid 343 through 348 Processing helix chain 't' and resid 348 through 355 Processing helix chain 't' and resid 359 through 372 Processing helix chain 't' and resid 379 through 397 Processing helix chain 't' and resid 400 through 414 Processing helix chain 't' and resid 417 through 431 removed outlier: 3.878A pdb=" N TYR t 421 " --> pdb=" O LEU t 417 " (cutoff:3.500A) Processing helix chain 't' and resid 433 through 446 Processing helix chain 't' and resid 452 through 464 Processing helix chain 't' and resid 468 through 476 Processing helix chain 't' and resid 487 through 494 Processing helix chain 't' and resid 497 through 525 removed outlier: 3.700A pdb=" N LYS t 515 " --> pdb=" O TYR t 511 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS t 516 " --> pdb=" O LEU t 512 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU t 524 " --> pdb=" O ASP t 520 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS t 525 " --> pdb=" O LEU t 521 " (cutoff:3.500A) Processing helix chain 't' and resid 531 through 536 removed outlier: 3.554A pdb=" N ILE t 536 " --> pdb=" O LYS t 532 " (cutoff:3.500A) Processing helix chain 't' and resid 537 through 559 removed outlier: 3.529A pdb=" N ASN t 559 " --> pdb=" O LEU t 555 " (cutoff:3.500A) Processing helix chain 't' and resid 560 through 571 Processing helix chain 't' and resid 574 through 582 removed outlier: 4.099A pdb=" N MET t 580 " --> pdb=" O HIS t 576 " (cutoff:3.500A) Processing helix chain 't' and resid 584 through 598 Processing helix chain 't' and resid 601 through 627 removed outlier: 4.351A pdb=" N SER t 627 " --> pdb=" O LEU t 623 " (cutoff:3.500A) Processing helix chain 't' and resid 646 through 669 Processing helix chain 't' and resid 690 through 699 Processing helix chain 't' and resid 700 through 706 Processing helix chain 't' and resid 713 through 723 removed outlier: 3.596A pdb=" N ASP t 717 " --> pdb=" O ASP t 713 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG t 723 " --> pdb=" O GLU t 719 " (cutoff:3.500A) Processing helix chain 't' and resid 727 through 741 Processing helix chain 't' and resid 745 through 759 removed outlier: 3.593A pdb=" N GLY t 749 " --> pdb=" O SER t 745 " (cutoff:3.500A) Processing helix chain 't' and resid 766 through 781 Processing helix chain 't' and resid 796 through 805 removed outlier: 3.847A pdb=" N PHE t 800 " --> pdb=" O ASP t 796 " (cutoff:3.500A) Processing helix chain 't' and resid 810 through 819 Processing helix chain 't' and resid 827 through 838 Processing helix chain 't' and resid 842 through 852 Processing helix chain 'u' and resid 9 through 11 No H-bonds generated for 'chain 'u' and resid 9 through 11' Processing helix chain 'u' and resid 12 through 22 Processing helix chain 'u' and resid 29 through 39 removed outlier: 3.536A pdb=" N TYR u 33 " --> pdb=" O MET u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 129 through 145 Processing helix chain 'u' and resid 158 through 166 Processing helix chain 'u' and resid 201 through 205 removed outlier: 3.973A pdb=" N THR u 205 " --> pdb=" O SER u 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 15 through 23 removed outlier: 3.678A pdb=" N LEU v 19 " --> pdb=" O ASN v 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA v 23 " --> pdb=" O LEU v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 38 Processing helix chain 'v' and resid 106 through 122 Processing helix chain 'v' and resid 136 through 147 removed outlier: 3.705A pdb=" N HIS v 145 " --> pdb=" O TRP v 141 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY v 146 " --> pdb=" O PHE v 142 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE v 147 " --> pdb=" O ILE v 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'u' and resid 4 through 7 removed outlier: 6.639A pdb=" N GLU u 90 " --> pdb=" O LEU u 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'u' and resid 4 through 7 removed outlier: 6.426A pdb=" N LYS u 99 " --> pdb=" O ILE u 115 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE u 115 " --> pdb=" O LYS u 99 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS u 153 " --> pdb=" O ILE u 115 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER u 117 " --> pdb=" O HIS u 153 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS u 191 " --> pdb=" O VAL u 173 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL u 173 " --> pdb=" O LYS u 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'v' and resid 6 through 9 removed outlier: 4.073A pdb=" N VAL v 58 " --> pdb=" O LEU v 78 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR v 66 " --> pdb=" O PRO v 70 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N VAL v 71 " --> pdb=" O VAL v 98 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL v 98 " --> pdb=" O VAL v 71 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY v 73 " --> pdb=" O LEU v 96 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU v 96 " --> pdb=" O GLY v 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL v 75 " --> pdb=" O GLU v 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE v 128 " --> pdb=" O ILE v 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE v 93 " --> pdb=" O PHE v 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR v 130 " --> pdb=" O ILE v 93 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE v 95 " --> pdb=" O TYR v 130 " (cutoff:3.500A) removed outlier: 14.983A pdb=" N GLY v 97 " --> pdb=" O PRO v 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'v' and resid 6 through 9 removed outlier: 4.073A pdb=" N VAL v 58 " --> pdb=" O LEU v 78 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR v 66 " --> pdb=" O PRO v 70 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N VAL v 71 " --> pdb=" O VAL v 98 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL v 98 " --> pdb=" O VAL v 71 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY v 73 " --> pdb=" O LEU v 96 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU v 96 " --> pdb=" O GLY v 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL v 75 " --> pdb=" O GLU v 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE v 128 " --> pdb=" O ILE v 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE v 93 " --> pdb=" O PHE v 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR v 130 " --> pdb=" O ILE v 93 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE v 95 " --> pdb=" O TYR v 130 " (cutoff:3.500A) removed outlier: 14.983A pdb=" N GLY v 97 " --> pdb=" O PRO v 132 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN v 166 " --> pdb=" O PHE v 157 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA v 168 " --> pdb=" O ASN v 155 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN v 155 " --> pdb=" O ALA v 168 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1679 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: 3.13 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3177 1.34 - 1.46: 1705 1.46 - 1.58: 4964 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 9909 Sorted by residual: bond pdb=" CA ASN t 639 " pdb=" C ASN t 639 " ideal model delta sigma weight residual 1.531 1.523 0.007 5.40e-03 3.43e+04 1.90e+00 bond pdb=" N GLY t 86 " pdb=" CA GLY t 86 " ideal model delta sigma weight residual 1.444 1.455 -0.011 9.60e-03 1.09e+04 1.31e+00 bond pdb=" CA GLU t 495 " pdb=" C GLU t 495 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.70e-01 bond pdb=" C GLN t 638 " pdb=" N ASN t 639 " ideal model delta sigma weight residual 1.325 1.333 -0.008 9.70e-03 1.06e+04 7.18e-01 bond pdb=" N ILE v 69 " pdb=" CA ILE v 69 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 7.16e-01 ... (remaining 9904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13212 1.37 - 2.73: 157 2.73 - 4.10: 27 4.10 - 5.47: 11 5.47 - 6.84: 3 Bond angle restraints: 13410 Sorted by residual: angle pdb=" C ASN t 643 " pdb=" CA ASN t 643 " pdb=" CB ASN t 643 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" C ASN t 639 " pdb=" CA ASN t 639 " pdb=" CB ASN t 639 " ideal model delta sigma weight residual 116.53 110.54 5.99 1.47e+00 4.63e-01 1.66e+01 angle pdb=" CA ASN t 643 " pdb=" C ASN t 643 " pdb=" N SER t 644 " ideal model delta sigma weight residual 119.98 116.92 3.06 8.50e-01 1.38e+00 1.29e+01 angle pdb=" CA ASN t 639 " pdb=" C ASN t 639 " pdb=" O ASN t 639 " ideal model delta sigma weight residual 118.33 120.33 -2.00 6.30e-01 2.52e+00 1.01e+01 angle pdb=" N LEU u 86 " pdb=" CA LEU u 86 " pdb=" C LEU u 86 " ideal model delta sigma weight residual 114.04 110.24 3.80 1.24e+00 6.50e-01 9.38e+00 ... (remaining 13405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 5748 15.08 - 30.15: 180 30.15 - 45.23: 57 45.23 - 60.31: 0 60.31 - 75.39: 5 Dihedral angle restraints: 5990 sinusoidal: 2331 harmonic: 3659 Sorted by residual: dihedral pdb=" CB LYS t 601 " pdb=" CG LYS t 601 " pdb=" CD LYS t 601 " pdb=" CE LYS t 601 " ideal model delta sinusoidal sigma weight residual 60.00 103.00 -43.00 3 1.50e+01 4.44e-03 7.72e+00 dihedral pdb=" CA LYS t 29 " pdb=" CB LYS t 29 " pdb=" CG LYS t 29 " pdb=" CD LYS t 29 " ideal model delta sinusoidal sigma weight residual 60.00 100.75 -40.75 3 1.50e+01 4.44e-03 7.27e+00 dihedral pdb=" CA LYS t 551 " pdb=" CB LYS t 551 " pdb=" CG LYS t 551 " pdb=" CD LYS t 551 " ideal model delta sinusoidal sigma weight residual -60.00 -98.67 38.67 3 1.50e+01 4.44e-03 6.82e+00 ... (remaining 5987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 956 0.025 - 0.050: 327 0.050 - 0.075: 125 0.075 - 0.100: 51 0.100 - 0.125: 20 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CA ILE u 5 " pdb=" N ILE u 5 " pdb=" C ILE u 5 " pdb=" CB ILE u 5 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE u 176 " pdb=" N ILE u 176 " pdb=" C ILE u 176 " pdb=" CB ILE u 176 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA VAL v 98 " pdb=" N VAL v 98 " pdb=" C VAL v 98 " pdb=" CB VAL v 98 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 1476 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL t 341 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO t 342 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO t 342 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO t 342 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER t 839 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO t 840 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO t 840 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO t 840 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU t 309 " 0.026 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO t 310 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO t 310 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO t 310 " 0.021 5.00e-02 4.00e+02 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2708 2.81 - 3.33: 9007 3.33 - 3.86: 15498 3.86 - 4.38: 16644 4.38 - 4.90: 30197 Nonbonded interactions: 74054 Sorted by model distance: nonbonded pdb=" OE2 GLU u 109 " pdb=" OH TYR u 149 " model vdw 2.289 3.040 nonbonded pdb=" OE1 GLU t 842 " pdb=" NE2 HIS t 844 " model vdw 2.295 3.120 nonbonded pdb=" O LYS t 356 " pdb=" OG SER t 360 " model vdw 2.324 3.040 nonbonded pdb=" OD2 ASP t 375 " pdb=" OG1 THR t 377 " model vdw 2.334 3.040 nonbonded pdb=" O LYS t 19 " pdb=" NE2 GLN t 23 " model vdw 2.345 3.120 ... (remaining 74049 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=0.77 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: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.890 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 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 : 0.001 0.022 9909 Z= 0.089 Angle : 0.403 6.837 13410 Z= 0.249 Chirality : 0.034 0.125 1479 Planarity : 0.003 0.040 1735 Dihedral : 8.701 75.387 3626 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.52 % Favored : 88.42 % Rotamer: Outliers : 0.10 % Allowed : 1.01 % Favored : 98.89 % 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: -1.81 (0.22), residues: 1226 helix: 0.03 (0.18), residues: 745 sheet: -1.69 (0.56), residues: 72 loop : -3.45 (0.25), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP t 385 HIS 0.002 0.000 HIS t 576 PHE 0.007 0.000 PHE t 800 TYR 0.012 0.001 TYR t 507 ARG 0.001 0.000 ARG u 142 Details of bonding type rmsd hydrogen bonds : bond 0.12643 ( 542) hydrogen bonds : angle 5.23447 ( 1679) covalent geometry : bond 0.00139 ( 9909) covalent geometry : angle 0.40304 (13410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.105 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: t 314 ILE cc_start: 0.7824 (mt) cc_final: 0.7207 (mt) REVERT: t 428 LEU cc_start: 0.8776 (mt) cc_final: 0.8530 (mt) REVERT: t 441 LEU cc_start: 0.7889 (tp) cc_final: 0.7180 (tp) REVERT: t 458 THR cc_start: 0.6485 (m) cc_final: 0.5834 (m) REVERT: t 543 ASN cc_start: 0.5120 (t0) cc_final: 0.4876 (t0) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2877 time to fit residues: 118.6309 Evaluate side-chains 164 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 23 GLN t 95 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 161 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 180 ASN ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 320 GLN t 347 ASN ** t 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 701 ASN t 735 ASN ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 153 HIS v 32 GLN v 59 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.239641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.223365 restraints weight = 54186.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.225015 restraints weight = 38630.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.226220 restraints weight = 28408.329| |-----------------------------------------------------------------------------| r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4745 r_free = 0.4745 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4743 r_free = 0.4743 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9909 Z= 0.198 Angle : 0.682 8.239 13410 Z= 0.351 Chirality : 0.041 0.170 1479 Planarity : 0.005 0.065 1735 Dihedral : 3.623 23.405 1346 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Rotamer: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % 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: -0.73 (0.23), residues: 1226 helix: 0.91 (0.19), residues: 734 sheet: -0.63 (0.58), residues: 79 loop : -3.12 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP t 385 HIS 0.009 0.002 HIS v 59 PHE 0.021 0.002 PHE t 345 TYR 0.024 0.002 TYR t 421 ARG 0.007 0.001 ARG u 135 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 542) hydrogen bonds : angle 4.10457 ( 1679) covalent geometry : bond 0.00426 ( 9909) covalent geometry : angle 0.68171 (13410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.068 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: t 206 MET cc_start: 0.9060 (mtm) cc_final: 0.8539 (mtt) REVERT: t 314 ILE cc_start: 0.9002 (mt) cc_final: 0.8531 (mt) REVERT: t 441 LEU cc_start: 0.8672 (tp) cc_final: 0.8200 (tp) REVERT: t 458 THR cc_start: 0.6684 (m) cc_final: 0.6400 (m) REVERT: t 593 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7886 (pp20) REVERT: t 694 ASP cc_start: 0.7511 (m-30) cc_final: 0.7193 (m-30) REVERT: u 16 MET cc_start: 0.6702 (mtm) cc_final: 0.6368 (mtm) REVERT: u 162 LEU cc_start: 0.7482 (mt) cc_final: 0.7260 (mt) REVERT: v 102 TYR cc_start: 0.3842 (m-80) cc_final: 0.3536 (m-80) REVERT: v 147 PHE cc_start: 0.9051 (m-80) cc_final: 0.8793 (m-10) REVERT: v 172 LYS cc_start: 0.6845 (pttt) cc_final: 0.6372 (mmtt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2226 time to fit residues: 64.0748 Evaluate side-chains 152 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 161 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 ASN t 481 ASN t 492 HIS t 543 ASN u 112 ASN u 200 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.225459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.209291 restraints weight = 54986.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.210984 restraints weight = 38791.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.212260 restraints weight = 28239.768| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9909 Z= 0.216 Angle : 0.722 6.878 13410 Z= 0.377 Chirality : 0.042 0.180 1479 Planarity : 0.005 0.047 1735 Dihedral : 4.173 24.292 1346 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 0.20 % Allowed : 3.32 % Favored : 96.48 % 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: -0.84 (0.23), residues: 1226 helix: 0.73 (0.18), residues: 742 sheet: -0.58 (0.59), residues: 74 loop : -3.06 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP t 113 HIS 0.007 0.002 HIS v 59 PHE 0.028 0.003 PHE u 139 TYR 0.066 0.002 TYR t 550 ARG 0.007 0.001 ARG u 125 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 542) hydrogen bonds : angle 4.28285 ( 1679) covalent geometry : bond 0.00439 ( 9909) covalent geometry : angle 0.72238 (13410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 1.128 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: t 22 ASP cc_start: 0.5932 (m-30) cc_final: 0.5664 (m-30) REVERT: t 97 LEU cc_start: 0.8989 (mt) cc_final: 0.8635 (mt) REVERT: t 206 MET cc_start: 0.9287 (mtm) cc_final: 0.8744 (mtm) REVERT: t 314 ILE cc_start: 0.9058 (mt) cc_final: 0.8485 (mt) REVERT: t 441 LEU cc_start: 0.8987 (tp) cc_final: 0.8552 (tp) REVERT: t 458 THR cc_start: 0.6990 (m) cc_final: 0.6707 (m) REVERT: t 694 ASP cc_start: 0.7859 (m-30) cc_final: 0.7415 (p0) REVERT: u 162 LEU cc_start: 0.7496 (mt) cc_final: 0.7253 (mt) REVERT: u 225 LEU cc_start: 0.8824 (mt) cc_final: 0.8580 (mt) REVERT: v 147 PHE cc_start: 0.9076 (m-80) cc_final: 0.8826 (m-10) REVERT: v 172 LYS cc_start: 0.6653 (pttt) cc_final: 0.6378 (mmtt) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.2222 time to fit residues: 58.8384 Evaluate side-chains 142 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 119 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 172 ASN t 219 ASN ** t 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.186645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.162496 restraints weight = 36564.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.166871 restraints weight = 24834.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.170314 restraints weight = 17912.790| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4546 r_free = 0.4546 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4546 r_free = 0.4546 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9909 Z= 0.155 Angle : 0.640 7.887 13410 Z= 0.327 Chirality : 0.040 0.129 1479 Planarity : 0.004 0.040 1735 Dihedral : 4.141 23.576 1346 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.98 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % 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: -0.64 (0.24), residues: 1226 helix: 0.83 (0.19), residues: 755 sheet: -0.73 (0.54), residues: 84 loop : -2.96 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP t 162 HIS 0.003 0.001 HIS t 413 PHE 0.023 0.002 PHE u 139 TYR 0.024 0.002 TYR t 550 ARG 0.005 0.001 ARG t 159 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 542) hydrogen bonds : angle 4.18546 ( 1679) covalent geometry : bond 0.00342 ( 9909) covalent geometry : angle 0.64021 (13410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.138 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: t 34 LYS cc_start: 0.8795 (tppt) cc_final: 0.8575 (tppt) REVERT: t 206 MET cc_start: 0.9421 (mtm) cc_final: 0.8690 (mtm) REVERT: t 314 ILE cc_start: 0.9031 (mt) cc_final: 0.8492 (mt) REVERT: t 441 LEU cc_start: 0.8974 (tp) cc_final: 0.8517 (tp) REVERT: t 567 GLN cc_start: 0.9194 (pt0) cc_final: 0.8172 (mm-40) REVERT: t 694 ASP cc_start: 0.7898 (m-30) cc_final: 0.7597 (m-30) REVERT: t 705 MET cc_start: 0.8918 (ptt) cc_final: 0.8575 (ptt) REVERT: u 95 TYR cc_start: 0.4430 (p90) cc_final: 0.4109 (p90) REVERT: u 162 LEU cc_start: 0.7672 (mt) cc_final: 0.7360 (mt) REVERT: u 225 LEU cc_start: 0.8968 (mt) cc_final: 0.8740 (mt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2345 time to fit residues: 57.6595 Evaluate side-chains 137 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 0.0970 chunk 99 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 overall best weight: 3.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 676 GLN u 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.186529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.163770 restraints weight = 38831.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.167980 restraints weight = 25994.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.171312 restraints weight = 18628.955| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4555 r_free = 0.4555 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9909 Z= 0.134 Angle : 0.607 7.511 13410 Z= 0.309 Chirality : 0.039 0.128 1479 Planarity : 0.004 0.047 1735 Dihedral : 4.100 23.806 1346 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1226 helix: 0.94 (0.19), residues: 753 sheet: -0.66 (0.54), residues: 86 loop : -2.87 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP t 162 HIS 0.003 0.001 HIS v 59 PHE 0.047 0.002 PHE u 45 TYR 0.026 0.001 TYR t 550 ARG 0.008 0.001 ARG t 246 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 542) hydrogen bonds : angle 4.03720 ( 1679) covalent geometry : bond 0.00308 ( 9909) covalent geometry : angle 0.60660 (13410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.105 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: t 22 ASP cc_start: 0.5578 (m-30) cc_final: 0.5336 (m-30) REVERT: t 97 LEU cc_start: 0.9090 (mt) cc_final: 0.8634 (mt) REVERT: t 158 TYR cc_start: 0.7970 (t80) cc_final: 0.6624 (m-80) REVERT: t 206 MET cc_start: 0.9398 (mtm) cc_final: 0.8750 (mtm) REVERT: t 314 ILE cc_start: 0.8996 (mt) cc_final: 0.8449 (mt) REVERT: t 567 GLN cc_start: 0.9149 (pt0) cc_final: 0.8149 (mm-40) REVERT: t 608 MET cc_start: 0.4827 (ttt) cc_final: 0.4606 (ttm) REVERT: t 694 ASP cc_start: 0.7903 (m-30) cc_final: 0.7587 (m-30) REVERT: t 705 MET cc_start: 0.8924 (ptt) cc_final: 0.8579 (ptt) REVERT: u 22 HIS cc_start: 0.7931 (m-70) cc_final: 0.7719 (m-70) REVERT: u 95 TYR cc_start: 0.4373 (p90) cc_final: 0.4131 (p90) REVERT: u 162 LEU cc_start: 0.7655 (mt) cc_final: 0.7321 (mt) REVERT: u 225 LEU cc_start: 0.9009 (mt) cc_final: 0.8787 (mt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2198 time to fit residues: 52.6937 Evaluate side-chains 134 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 99 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 446 GLN t 481 ASN t 572 GLN u 136 GLN u 153 HIS ** v 166 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 = 0.4710 r_free = 0.4710 target = 0.185054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.161308 restraints weight = 36634.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.165751 restraints weight = 24560.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.169100 restraints weight = 17547.665| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9909 Z= 0.124 Angle : 0.606 6.925 13410 Z= 0.309 Chirality : 0.039 0.156 1479 Planarity : 0.004 0.045 1735 Dihedral : 4.067 23.329 1346 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1226 helix: 1.01 (0.19), residues: 749 sheet: -0.64 (0.55), residues: 86 loop : -2.76 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP t 162 HIS 0.006 0.001 HIS u 36 PHE 0.036 0.002 PHE u 45 TYR 0.021 0.002 TYR t 550 ARG 0.007 0.001 ARG t 246 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 542) hydrogen bonds : angle 4.01826 ( 1679) covalent geometry : bond 0.00278 ( 9909) covalent geometry : angle 0.60633 (13410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.475 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: t 22 ASP cc_start: 0.5604 (m-30) cc_final: 0.5333 (m-30) REVERT: t 34 LYS cc_start: 0.8893 (tppt) cc_final: 0.8661 (tppt) REVERT: t 152 TRP cc_start: 0.7565 (t60) cc_final: 0.6915 (t60) REVERT: t 158 TYR cc_start: 0.8104 (t80) cc_final: 0.6861 (m-80) REVERT: t 206 MET cc_start: 0.9424 (mtm) cc_final: 0.8863 (mtp) REVERT: t 314 ILE cc_start: 0.9026 (mt) cc_final: 0.8485 (mt) REVERT: t 567 GLN cc_start: 0.9129 (pt0) cc_final: 0.8081 (mm-40) REVERT: t 608 MET cc_start: 0.4920 (ttt) cc_final: 0.4539 (ttm) REVERT: t 694 ASP cc_start: 0.7955 (m-30) cc_final: 0.7627 (m-30) REVERT: t 700 TYR cc_start: 0.6499 (t80) cc_final: 0.6202 (t80) REVERT: t 705 MET cc_start: 0.8763 (ptt) cc_final: 0.8314 (ptt) REVERT: u 49 THR cc_start: 0.9209 (m) cc_final: 0.8907 (p) REVERT: u 162 LEU cc_start: 0.7635 (mt) cc_final: 0.7294 (mt) REVERT: u 225 LEU cc_start: 0.9023 (mt) cc_final: 0.8801 (mt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2444 time to fit residues: 56.4916 Evaluate side-chains 132 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 392 GLN t 481 ASN t 544 GLN u 136 GLN ** v 166 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 = 0.5091 r_free = 0.5091 target = 0.217681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.201563 restraints weight = 54100.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.203302 restraints weight = 38232.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.204594 restraints weight = 27990.895| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4566 r_free = 0.4566 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4565 r_free = 0.4565 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9909 Z= 0.167 Angle : 0.686 9.766 13410 Z= 0.353 Chirality : 0.042 0.332 1479 Planarity : 0.005 0.049 1735 Dihedral : 4.489 22.421 1346 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.28 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.62 (0.24), residues: 1226 helix: 0.84 (0.19), residues: 743 sheet: -0.78 (0.57), residues: 81 loop : -2.78 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 162 HIS 0.007 0.002 HIS u 36 PHE 0.032 0.002 PHE u 45 TYR 0.025 0.002 TYR t 817 ARG 0.007 0.001 ARG t 464 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 542) hydrogen bonds : angle 4.22426 ( 1679) covalent geometry : bond 0.00363 ( 9909) covalent geometry : angle 0.68579 (13410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.027 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: t 22 ASP cc_start: 0.5823 (m-30) cc_final: 0.5528 (m-30) REVERT: t 34 LYS cc_start: 0.8801 (tppt) cc_final: 0.8587 (tppt) REVERT: t 152 TRP cc_start: 0.8186 (t60) cc_final: 0.7701 (t60) REVERT: t 158 TYR cc_start: 0.7989 (t80) cc_final: 0.6943 (m-80) REVERT: t 206 MET cc_start: 0.9277 (mtm) cc_final: 0.8647 (mtm) REVERT: t 314 ILE cc_start: 0.9062 (mt) cc_final: 0.8477 (mt) REVERT: t 608 MET cc_start: 0.5421 (ttt) cc_final: 0.5108 (ttm) REVERT: t 705 MET cc_start: 0.8634 (ptt) cc_final: 0.8229 (ptt) REVERT: u 49 THR cc_start: 0.9180 (m) cc_final: 0.8896 (p) REVERT: u 95 TYR cc_start: 0.4721 (p90) cc_final: 0.4396 (p90) REVERT: u 100 MET cc_start: 0.6055 (mmm) cc_final: 0.5163 (tpp) REVERT: u 127 MET cc_start: 0.1097 (mtt) cc_final: 0.0854 (mtt) REVERT: u 162 LEU cc_start: 0.7852 (mt) cc_final: 0.7526 (mt) REVERT: v 147 PHE cc_start: 0.9095 (m-10) cc_final: 0.8871 (m-10) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2247 time to fit residues: 51.1370 Evaluate side-chains 124 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 88 optimal weight: 0.0970 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 119 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 23 ASN u 136 GLN ** v 166 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 = 0.5114 r_free = 0.5114 target = 0.220681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.204119 restraints weight = 53881.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.205835 restraints weight = 38026.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.207148 restraints weight = 27814.722| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4584 r_free = 0.4584 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4584 r_free = 0.4584 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9909 Z= 0.133 Angle : 0.639 7.722 13410 Z= 0.328 Chirality : 0.040 0.160 1479 Planarity : 0.004 0.042 1735 Dihedral : 4.352 22.795 1346 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.71 % Favored : 94.13 % 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: -0.54 (0.24), residues: 1226 helix: 0.91 (0.19), residues: 751 sheet: -0.90 (0.56), residues: 81 loop : -2.79 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP t 162 HIS 0.003 0.001 HIS t 413 PHE 0.027 0.002 PHE u 45 TYR 0.028 0.002 TYR t 700 ARG 0.006 0.001 ARG t 246 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 542) hydrogen bonds : angle 4.15714 ( 1679) covalent geometry : bond 0.00305 ( 9909) covalent geometry : angle 0.63927 (13410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.148 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: t 22 ASP cc_start: 0.5766 (m-30) cc_final: 0.5480 (m-30) REVERT: t 34 LYS cc_start: 0.8690 (tppt) cc_final: 0.8467 (tppt) REVERT: t 152 TRP cc_start: 0.8181 (t60) cc_final: 0.7394 (t60) REVERT: t 158 TYR cc_start: 0.7813 (t80) cc_final: 0.6977 (m-80) REVERT: t 206 MET cc_start: 0.9303 (mtm) cc_final: 0.8643 (mtt) REVERT: t 314 ILE cc_start: 0.9005 (mt) cc_final: 0.8382 (mt) REVERT: t 375 ASP cc_start: 0.6561 (t70) cc_final: 0.6171 (t70) REVERT: t 608 MET cc_start: 0.5182 (ttt) cc_final: 0.4711 (ttm) REVERT: t 694 ASP cc_start: 0.8000 (m-30) cc_final: 0.7696 (m-30) REVERT: t 705 MET cc_start: 0.8529 (ptt) cc_final: 0.8161 (ptt) REVERT: u 23 ASN cc_start: 0.8265 (m110) cc_final: 0.8043 (m110) REVERT: u 38 LEU cc_start: 0.7954 (mt) cc_final: 0.7662 (mp) REVERT: u 49 THR cc_start: 0.9127 (m) cc_final: 0.8811 (p) REVERT: u 100 MET cc_start: 0.6179 (mmm) cc_final: 0.5231 (tpp) REVERT: u 162 LEU cc_start: 0.7789 (mt) cc_final: 0.7478 (mt) REVERT: v 147 PHE cc_start: 0.9096 (m-10) cc_final: 0.8851 (m-10) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2491 time to fit residues: 57.1540 Evaluate side-chains 129 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 GLN v 156 ASN ** v 166 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 = 0.5100 r_free = 0.5100 target = 0.218702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5097 r_free = 0.5097 target = 0.202688 restraints weight = 53565.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.204385 restraints weight = 37852.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.205612 restraints weight = 27507.670| |-----------------------------------------------------------------------------| r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4577 r_free = 0.4577 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4577 r_free = 0.4577 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9909 Z= 0.145 Angle : 0.659 9.976 13410 Z= 0.338 Chirality : 0.041 0.176 1479 Planarity : 0.004 0.049 1735 Dihedral : 4.359 22.383 1346 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.50 (0.24), residues: 1226 helix: 0.96 (0.19), residues: 744 sheet: -1.01 (0.56), residues: 81 loop : -2.72 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP t 162 HIS 0.004 0.001 HIS t 844 PHE 0.027 0.002 PHE u 45 TYR 0.034 0.002 TYR t 700 ARG 0.016 0.001 ARG t 606 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 542) hydrogen bonds : angle 4.17024 ( 1679) covalent geometry : bond 0.00333 ( 9909) covalent geometry : angle 0.65936 (13410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.140 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: t 22 ASP cc_start: 0.5689 (m-30) cc_final: 0.5411 (m-30) REVERT: t 152 TRP cc_start: 0.8263 (t60) cc_final: 0.7616 (t60) REVERT: t 158 TYR cc_start: 0.7846 (t80) cc_final: 0.7032 (m-80) REVERT: t 200 GLU cc_start: 0.8720 (pm20) cc_final: 0.8478 (pm20) REVERT: t 206 MET cc_start: 0.9306 (mtm) cc_final: 0.8664 (mtm) REVERT: t 314 ILE cc_start: 0.9041 (mt) cc_final: 0.8427 (mt) REVERT: t 375 ASP cc_start: 0.6524 (t70) cc_final: 0.6143 (t70) REVERT: t 402 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8683 (tptp) REVERT: t 580 MET cc_start: -0.0135 (mmt) cc_final: -0.0476 (mmt) REVERT: t 608 MET cc_start: 0.5220 (ttt) cc_final: 0.4832 (ttm) REVERT: t 694 ASP cc_start: 0.8070 (m-30) cc_final: 0.7753 (m-30) REVERT: t 705 MET cc_start: 0.8518 (ptt) cc_final: 0.8049 (ptt) REVERT: u 23 ASN cc_start: 0.8113 (m110) cc_final: 0.7788 (m110) REVERT: u 38 LEU cc_start: 0.8000 (mt) cc_final: 0.7793 (mm) REVERT: u 49 THR cc_start: 0.9160 (m) cc_final: 0.8829 (p) REVERT: u 79 ILE cc_start: 0.8414 (mp) cc_final: 0.8129 (tp) REVERT: u 95 TYR cc_start: 0.4528 (p90) cc_final: 0.4227 (p90) REVERT: u 155 ARG cc_start: 0.7524 (mtt-85) cc_final: 0.7302 (mtt-85) REVERT: u 162 LEU cc_start: 0.7828 (mt) cc_final: 0.7528 (mt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2485 time to fit residues: 58.8389 Evaluate side-chains 136 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 GLN ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.219964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.203879 restraints weight = 53730.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.205595 restraints weight = 38034.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.206815 restraints weight = 27949.502| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4592 r_free = 0.4592 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4592 r_free = 0.4592 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.8166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9909 Z= 0.128 Angle : 0.646 8.200 13410 Z= 0.331 Chirality : 0.042 0.291 1479 Planarity : 0.004 0.042 1735 Dihedral : 4.281 22.042 1346 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.71 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.42 (0.24), residues: 1226 helix: 1.02 (0.19), residues: 750 sheet: -0.95 (0.57), residues: 81 loop : -2.76 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP t 385 HIS 0.006 0.001 HIS t 576 PHE 0.029 0.002 PHE t 718 TYR 0.037 0.002 TYR t 700 ARG 0.007 0.001 ARG t 102 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 542) hydrogen bonds : angle 4.05500 ( 1679) covalent geometry : bond 0.00289 ( 9909) covalent geometry : angle 0.64648 (13410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.013 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: t 22 ASP cc_start: 0.5633 (m-30) cc_final: 0.5350 (m-30) REVERT: t 97 LEU cc_start: 0.8749 (mt) cc_final: 0.8498 (mt) REVERT: t 108 LYS cc_start: 0.8843 (mppt) cc_final: 0.8408 (mppt) REVERT: t 152 TRP cc_start: 0.8167 (t60) cc_final: 0.7426 (t60) REVERT: t 158 TYR cc_start: 0.7575 (t80) cc_final: 0.7019 (m-80) REVERT: t 200 GLU cc_start: 0.8612 (pm20) cc_final: 0.8366 (pm20) REVERT: t 206 MET cc_start: 0.9319 (mtm) cc_final: 0.8758 (mtp) REVERT: t 208 LYS cc_start: 0.6413 (tttt) cc_final: 0.6144 (tttt) REVERT: t 314 ILE cc_start: 0.9012 (mt) cc_final: 0.8406 (mt) REVERT: t 375 ASP cc_start: 0.6436 (t70) cc_final: 0.6038 (t70) REVERT: t 402 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8626 (tptp) REVERT: t 580 MET cc_start: 0.0279 (mmt) cc_final: -0.0062 (mmt) REVERT: t 608 MET cc_start: 0.4948 (ttt) cc_final: 0.4532 (ttm) REVERT: t 694 ASP cc_start: 0.8050 (m-30) cc_final: 0.7741 (m-30) REVERT: t 705 MET cc_start: 0.8382 (ptt) cc_final: 0.7699 (ptt) REVERT: u 23 ASN cc_start: 0.8129 (m110) cc_final: 0.7906 (m110) REVERT: u 49 THR cc_start: 0.9083 (m) cc_final: 0.8748 (p) REVERT: u 79 ILE cc_start: 0.8377 (mp) cc_final: 0.8147 (tp) REVERT: u 100 MET cc_start: 0.5909 (mmm) cc_final: 0.4934 (tpp) REVERT: u 162 LEU cc_start: 0.7797 (mt) cc_final: 0.7571 (mt) REVERT: v 150 VAL cc_start: 0.8421 (t) cc_final: 0.8215 (t) REVERT: v 172 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8306 (mmmt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2434 time to fit residues: 56.8558 Evaluate side-chains 133 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 104 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 219 ASN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 GLN ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 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 = 0.5079 r_free = 0.5079 target = 0.216415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.200311 restraints weight = 53449.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.202040 restraints weight = 37935.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.203282 restraints weight = 27555.922| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 0.8526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9909 Z= 0.142 Angle : 0.660 8.051 13410 Z= 0.341 Chirality : 0.043 0.267 1479 Planarity : 0.004 0.048 1735 Dihedral : 4.415 21.164 1346 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.47 (0.24), residues: 1226 helix: 0.98 (0.19), residues: 743 sheet: -1.01 (0.57), residues: 75 loop : -2.68 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP t 162 HIS 0.006 0.001 HIS t 53 PHE 0.023 0.002 PHE u 45 TYR 0.035 0.002 TYR t 700 ARG 0.007 0.001 ARG t 606 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 542) hydrogen bonds : angle 4.18663 ( 1679) covalent geometry : bond 0.00320 ( 9909) covalent geometry : angle 0.65976 (13410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3216.85 seconds wall clock time: 56 minutes 56.68 seconds (3416.68 seconds total)