Starting phenix.real_space_refine on Fri Feb 14 03:26:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hd5_0201/02_2025/6hd5_0201_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hd5_0201/02_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_0201/02_2025/6hd5_0201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hd5_0201/02_2025/6hd5_0201.map" model { file = "/net/cci-nas-00/data/ceres_data/6hd5_0201/02_2025/6hd5_0201_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hd5_0201/02_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-5592/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: 6.92, per 1000 atoms: 0.71 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: 2.52 Conformation dependent library (CDL) restraints added in 1.2 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: 1.13 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: 3.23 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 3.480 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.120 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- 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= 0.087 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 *********************** 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 : 1.013 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: 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: 0.2874 time to fit residues: 118.5485 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 : 1.131 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.223407 restraints weight = 54186.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.224981 restraints weight = 38421.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.226189 restraints weight = 28648.289| |-----------------------------------------------------------------------------| 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= 0.273 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 *********************** 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 : 1.090 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: 0.9062 (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: 0.8673 (tp) cc_final: 0.8202 (tp) REVERT: t 458 THR cc_start: 0.6681 (m) cc_final: 0.6397 (m) REVERT: t 593 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7886 (pp20) REVERT: t 694 ASP cc_start: 0.7513 (m-30) cc_final: 0.7196 (m-30) REVERT: u 16 MET cc_start: 0.6705 (mtm) cc_final: 0.6370 (mtm) REVERT: u 162 LEU cc_start: 0.7484 (mt) cc_final: 0.7263 (mt) REVERT: v 102 TYR cc_start: 0.3841 (m-80) cc_final: 0.3535 (m-80) REVERT: v 147 PHE cc_start: 0.9048 (m-80) cc_final: 0.8788 (m-10) REVERT: v 172 LYS cc_start: 0.6849 (pttt) cc_final: 0.6374 (mmtt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2289 time to fit residues: 65.9635 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 : 1.016 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 5.9590 ------------------------------------------------------------------------------- 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 t 291 ASN ** t 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.5164 r_free = 0.5164 target = 0.229313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5169 r_free = 0.5169 target = 0.213017 restraints weight = 54898.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.214733 restraints weight = 38322.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.215995 restraints weight = 27863.671| |-----------------------------------------------------------------------------| r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4652 r_free = 0.4652 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4652 r_free = 0.4652 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9909 Z= 0.242 Angle : 0.672 7.073 13410 Z= 0.348 Chirality : 0.041 0.139 1479 Planarity : 0.004 0.043 1735 Dihedral : 3.921 24.642 1346 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.95 % Favored : 93.72 % Rotamer: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1226 helix: 0.88 (0.19), residues: 745 sheet: -0.52 (0.59), residues: 74 loop : -2.98 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP t 113 HIS 0.007 0.001 HIS v 59 PHE 0.023 0.003 PHE v 60 TYR 0.060 0.002 TYR t 550 ARG 0.006 0.001 ARG u 125 *********************** 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 185 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.038 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: 0.5847 (m-30) cc_final: 0.5577 (m-30) REVERT: t 34 LYS cc_start: 0.8760 (tppt) cc_final: 0.8532 (tppt) REVERT: t 97 LEU cc_start: 0.8995 (mt) cc_final: 0.8701 (mt) REVERT: t 206 MET cc_start: 0.9265 (mtm) cc_final: 0.8739 (mtm) REVERT: t 314 ILE cc_start: 0.9036 (mt) cc_final: 0.8472 (mt) REVERT: t 441 LEU cc_start: 0.8947 (tp) cc_final: 0.8505 (tp) REVERT: t 458 THR cc_start: 0.6858 (m) cc_final: 0.6570 (m) REVERT: t 694 ASP cc_start: 0.7769 (m-30) cc_final: 0.7468 (m-30) REVERT: u 10 ILE cc_start: 0.2265 (tt) cc_final: 0.2048 (mt) REVERT: u 16 MET cc_start: 0.6215 (mtm) cc_final: 0.6007 (mtm) REVERT: u 95 TYR cc_start: 0.4476 (p90) cc_final: 0.4240 (p90) REVERT: u 123 THR cc_start: 0.4991 (p) cc_final: 0.4786 (p) REVERT: u 162 LEU cc_start: 0.7483 (mt) cc_final: 0.7185 (mt) REVERT: u 225 LEU cc_start: 0.8771 (mt) cc_final: 0.8532 (mt) REVERT: v 128 PHE cc_start: 0.5173 (p90) cc_final: 0.4810 (p90) REVERT: v 147 PHE cc_start: 0.9002 (m-80) cc_final: 0.8756 (m-10) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2180 time to fit residues: 56.5228 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 : 1.025 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 62 optimal weight: 0.0070 chunk 41 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 430 HIS t 572 GLN u 200 GLN v 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.190212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.167106 restraints weight = 37810.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.171439 restraints weight = 25789.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.174783 restraints weight = 18609.135| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4585 r_free = 0.4585 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4585 r_free = 0.4585 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.6064 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= 0.184 Angle : 0.594 8.100 13410 Z= 0.301 Chirality : 0.039 0.125 1479 Planarity : 0.004 0.039 1735 Dihedral : 3.813 24.409 1346 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.94 % Rotamer: Outliers : 0.10 % Allowed : 2.11 % Favored : 97.78 % 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: -0.40 (0.24), residues: 1226 helix: 1.06 (0.19), residues: 754 sheet: -0.54 (0.56), residues: 81 loop : -2.94 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP t 162 HIS 0.003 0.001 HIS v 59 PHE 0.018 0.002 PHE u 139 TYR 0.025 0.001 TYR t 550 ARG 0.005 0.001 ARG u 135 *********************** 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 185 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.222 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 34 LYS cc_start: 0.8751 (tppt) cc_final: 0.8510 (tppt) REVERT: t 206 MET cc_start: 0.9398 (mtm) cc_final: 0.8677 (mtm) REVERT: t 314 ILE cc_start: 0.9002 (mt) cc_final: 0.8485 (mt) REVERT: t 441 LEU cc_start: 0.8961 (tp) cc_final: 0.8541 (tp) REVERT: t 458 THR cc_start: 0.6916 (m) cc_final: 0.6649 (m) REVERT: t 567 GLN cc_start: 0.9233 (pt0) cc_final: 0.8706 (mm-40) REVERT: t 690 THR cc_start: 0.8635 (p) cc_final: 0.8397 (p) REVERT: t 694 ASP cc_start: 0.7759 (m-30) cc_final: 0.7445 (m-30) REVERT: t 705 MET cc_start: 0.8836 (ptt) cc_final: 0.8497 (ptt) REVERT: u 16 MET cc_start: 0.6118 (mtm) cc_final: 0.5877 (mtm) REVERT: u 95 TYR cc_start: 0.4231 (p90) cc_final: 0.3915 (p90) REVERT: u 162 LEU cc_start: 0.7536 (mt) cc_final: 0.7220 (mt) REVERT: u 225 LEU cc_start: 0.8956 (mt) cc_final: 0.8741 (mt) REVERT: v 128 PHE cc_start: 0.5205 (p90) cc_final: 0.4989 (p90) REVERT: v 147 PHE cc_start: 0.9101 (m-80) cc_final: 0.8890 (m-10) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2234 time to fit residues: 57.3311 Evaluate side-chains 145 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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: 0.6980 chunk 56 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 104 optimal weight: 0.0470 chunk 76 optimal weight: 0.3980 overall best weight: 0.6282 ------------------------------------------------------------------------------- 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 172 ASN t 291 ASN t 446 GLN u 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.234336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.217838 restraints weight = 53501.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.219568 restraints weight = 38164.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5254 r_free = 0.5254 target = 0.220796 restraints weight = 27731.057| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4690 r_free = 0.4690 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4690 r_free = 0.4690 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9909 Z= 0.151 Angle : 0.573 8.192 13410 Z= 0.286 Chirality : 0.039 0.278 1479 Planarity : 0.003 0.044 1735 Dihedral : 3.653 24.532 1346 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: -0.15 (0.24), residues: 1226 helix: 1.20 (0.19), residues: 758 sheet: -0.55 (0.55), residues: 86 loop : -2.76 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP t 162 HIS 0.003 0.001 HIS v 59 PHE 0.030 0.001 PHE v 114 TYR 0.023 0.001 TYR t 550 ARG 0.007 0.001 ARG t 148 *********************** 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 178 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.049 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: t 34 LYS cc_start: 0.8655 (tppt) cc_final: 0.8415 (tppt) REVERT: t 97 LEU cc_start: 0.9029 (mt) cc_final: 0.8614 (mt) REVERT: t 152 TRP cc_start: 0.7676 (t60) cc_final: 0.7453 (t60) REVERT: t 206 MET cc_start: 0.9279 (mtm) cc_final: 0.8622 (mtm) REVERT: t 314 ILE cc_start: 0.8932 (mt) cc_final: 0.8357 (mt) REVERT: t 567 GLN cc_start: 0.9181 (pt0) cc_final: 0.8723 (mm-40) REVERT: t 690 THR cc_start: 0.8544 (p) cc_final: 0.8278 (p) REVERT: t 694 ASP cc_start: 0.7722 (m-30) cc_final: 0.7412 (m-30) REVERT: t 705 MET cc_start: 0.8632 (ptt) cc_final: 0.8291 (ptt) REVERT: t 820 ARG cc_start: 0.6424 (ptt-90) cc_final: 0.6069 (ptt90) REVERT: u 162 LEU cc_start: 0.7714 (mt) cc_final: 0.7415 (mt) REVERT: u 192 LYS cc_start: 0.7762 (tptp) cc_final: 0.7348 (mmmm) REVERT: u 225 LEU cc_start: 0.8798 (mt) cc_final: 0.8580 (mt) REVERT: v 147 PHE cc_start: 0.9021 (m-80) cc_final: 0.8799 (m-10) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2226 time to fit residues: 55.6260 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 : 1.067 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 t 291 ASN t 544 GLN t 676 GLN u 136 GLN ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 153 HIS u 200 GLN ** v 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.181758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.159054 restraints weight = 38752.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.163381 restraints weight = 25827.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.166560 restraints weight = 18344.375| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4506 r_free = 0.4506 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4506 r_free = 0.4506 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9909 Z= 0.269 Angle : 0.726 7.629 13410 Z= 0.375 Chirality : 0.042 0.231 1479 Planarity : 0.005 0.052 1735 Dihedral : 4.490 22.905 1346 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.04 % Favored : 93.80 % Rotamer: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % 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: -0.65 (0.23), residues: 1226 helix: 0.80 (0.19), residues: 746 sheet: -0.62 (0.56), residues: 81 loop : -2.82 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP t 162 HIS 0.008 0.002 HIS u 36 PHE 0.028 0.003 PHE u 139 TYR 0.022 0.002 TYR t 550 ARG 0.008 0.001 ARG t 148 *********************** 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 163 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.153 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: t 22 ASP cc_start: 0.5683 (m-30) cc_final: 0.5408 (m-30) REVERT: t 97 LEU cc_start: 0.9125 (mt) cc_final: 0.8721 (mt) REVERT: t 152 TRP cc_start: 0.7727 (t60) cc_final: 0.7065 (t60) REVERT: t 206 MET cc_start: 0.9352 (mtm) cc_final: 0.8652 (mtm) REVERT: t 314 ILE cc_start: 0.9107 (mt) cc_final: 0.8598 (mt) REVERT: t 375 ASP cc_start: 0.6714 (t70) cc_final: 0.6391 (t70) REVERT: t 694 ASP cc_start: 0.8001 (m-30) cc_final: 0.7684 (m-30) REVERT: t 700 TYR cc_start: 0.6888 (t80) cc_final: 0.6651 (t80) REVERT: t 705 MET cc_start: 0.8791 (ptt) cc_final: 0.8490 (ptt) REVERT: u 95 TYR cc_start: 0.4773 (p90) cc_final: 0.4333 (p90) REVERT: u 121 MET cc_start: 0.1344 (tpt) cc_final: 0.1140 (tpt) REVERT: u 162 LEU cc_start: 0.7632 (mt) cc_final: 0.7392 (mt) REVERT: u 192 LYS cc_start: 0.7802 (tptp) cc_final: 0.7324 (mmmm) REVERT: u 225 LEU cc_start: 0.9007 (mt) cc_final: 0.8785 (mt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2225 time to fit residues: 50.6195 Evaluate side-chains 131 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 392 GLN t 481 ASN ** u 136 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 = 0.5064 r_free = 0.5064 target = 0.215135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.199034 restraints weight = 54541.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.200749 restraints weight = 38179.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.202018 restraints weight = 27791.559| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4532 r_free = 0.4532 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 = 0.4532 r_free = 0.4532 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.7982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9909 Z= 0.285 Angle : 0.741 9.731 13410 Z= 0.384 Chirality : 0.043 0.287 1479 Planarity : 0.005 0.051 1735 Dihedral : 4.798 26.897 1346 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.01 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1226 helix: 0.61 (0.19), residues: 755 sheet: -1.13 (0.54), residues: 81 loop : -2.97 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP v 141 HIS 0.005 0.002 HIS u 206 PHE 0.046 0.003 PHE u 45 TYR 0.044 0.002 TYR t 461 ARG 0.009 0.001 ARG t 82 *********************** 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 166 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.079 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: t 22 ASP cc_start: 0.5975 (m-30) cc_final: 0.5668 (m-30) REVERT: t 34 LYS cc_start: 0.8881 (tppt) cc_final: 0.8668 (tppt) REVERT: t 152 TRP cc_start: 0.7612 (t60) cc_final: 0.7278 (t60) REVERT: t 206 MET cc_start: 0.9343 (mtm) cc_final: 0.8695 (mtm) REVERT: t 314 ILE cc_start: 0.9104 (mt) cc_final: 0.8519 (mt) REVERT: t 375 ASP cc_start: 0.7057 (t70) cc_final: 0.6652 (t70) REVERT: t 705 MET cc_start: 0.8604 (ptt) cc_final: 0.8213 (ptt) REVERT: u 38 LEU cc_start: 0.8137 (mt) cc_final: 0.7817 (mp) REVERT: u 49 THR cc_start: 0.9197 (m) cc_final: 0.8888 (p) REVERT: u 100 MET cc_start: 0.6230 (mmm) cc_final: 0.5304 (tpp) REVERT: u 162 LEU cc_start: 0.7855 (mt) cc_final: 0.7506 (mt) REVERT: u 192 LYS cc_start: 0.7978 (tptp) cc_final: 0.7709 (mmmt) REVERT: u 225 LEU cc_start: 0.8915 (mt) cc_final: 0.8704 (mt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2467 time to fit residues: 57.4917 Evaluate side-chains 127 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 88 optimal weight: 40.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 GLN ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.216506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.200727 restraints weight = 54333.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.202708 restraints weight = 39563.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.204478 restraints weight = 25775.748| |-----------------------------------------------------------------------------| r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4569 r_free = 0.4569 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 = 0.4569 r_free = 0.4569 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.8197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 9909 Z= 0.225 Angle : 0.671 8.767 13410 Z= 0.344 Chirality : 0.042 0.192 1479 Planarity : 0.004 0.043 1735 Dihedral : 4.619 22.878 1346 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.88 % 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: -0.71 (0.24), residues: 1226 helix: 0.80 (0.19), residues: 750 sheet: -1.25 (0.52), residues: 81 loop : -2.85 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP v 141 HIS 0.006 0.001 HIS t 430 PHE 0.029 0.002 PHE u 45 TYR 0.034 0.002 TYR t 128 ARG 0.015 0.001 ARG t 820 *********************** 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 164 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.132 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: 0.5881 (m-30) cc_final: 0.5551 (m-30) REVERT: t 34 LYS cc_start: 0.8769 (tppt) cc_final: 0.8544 (tppt) REVERT: t 97 LEU cc_start: 0.9084 (mt) cc_final: 0.8828 (mt) REVERT: t 128 TYR cc_start: 0.8762 (m-80) cc_final: 0.8480 (m-80) REVERT: t 152 TRP cc_start: 0.7611 (t60) cc_final: 0.7297 (t60) REVERT: t 206 MET cc_start: 0.9351 (mtm) cc_final: 0.8786 (mtp) REVERT: t 314 ILE cc_start: 0.9074 (mt) cc_final: 0.8483 (mt) REVERT: t 375 ASP cc_start: 0.6873 (t70) cc_final: 0.6445 (t70) REVERT: t 700 TYR cc_start: 0.6924 (t80) cc_final: 0.6505 (t80) REVERT: t 705 MET cc_start: 0.8525 (ptt) cc_final: 0.8088 (ptt) REVERT: u 22 HIS cc_start: 0.7996 (m-70) cc_final: 0.7783 (m-70) REVERT: u 49 THR cc_start: 0.9118 (m) cc_final: 0.8808 (p) REVERT: u 100 MET cc_start: 0.6004 (mmm) cc_final: 0.5128 (tpp) REVERT: u 121 MET cc_start: 0.1733 (tpt) cc_final: 0.1509 (tpt) REVERT: u 192 LYS cc_start: 0.7925 (tptp) cc_final: 0.7543 (mmmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2257 time to fit residues: 51.6256 Evaluate side-chains 131 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 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 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.209265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.193341 restraints weight = 54088.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.195047 restraints weight = 38239.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.196308 restraints weight = 28143.987| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4493 r_free = 0.4493 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4493 r_free = 0.4493 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9909 Z= 0.285 Angle : 0.767 9.723 13410 Z= 0.395 Chirality : 0.045 0.195 1479 Planarity : 0.005 0.047 1735 Dihedral : 5.068 23.835 1346 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.83 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.23), residues: 1226 helix: 0.53 (0.19), residues: 751 sheet: -1.32 (0.51), residues: 81 loop : -3.06 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP v 141 HIS 0.008 0.002 HIS u 206 PHE 0.031 0.003 PHE u 45 TYR 0.030 0.002 TYR t 128 ARG 0.012 0.001 ARG t 159 *********************** 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 162 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.972 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: 0.5989 (m-30) cc_final: 0.5613 (m-30) REVERT: t 152 TRP cc_start: 0.8211 (t60) cc_final: 0.7812 (t60) REVERT: t 206 MET cc_start: 0.9299 (mtm) cc_final: 0.8886 (mtp) REVERT: t 209 ASN cc_start: 0.9161 (m110) cc_final: 0.8956 (t0) REVERT: t 314 ILE cc_start: 0.9152 (mt) cc_final: 0.8607 (mt) REVERT: t 375 ASP cc_start: 0.7028 (t70) cc_final: 0.6595 (t70) REVERT: t 441 LEU cc_start: 0.9088 (tp) cc_final: 0.8862 (tp) REVERT: t 458 THR cc_start: 0.7552 (m) cc_final: 0.7327 (m) REVERT: t 580 MET cc_start: 0.0515 (tpp) cc_final: 0.0065 (tpp) REVERT: t 608 MET cc_start: 0.6277 (ttt) cc_final: 0.5904 (ttm) REVERT: t 694 ASP cc_start: 0.8101 (m-30) cc_final: 0.7768 (m-30) REVERT: u 22 HIS cc_start: 0.8058 (m-70) cc_final: 0.7837 (m-70) REVERT: u 29 MET cc_start: 0.2798 (tpp) cc_final: 0.2464 (mmp) REVERT: u 162 LEU cc_start: 0.7771 (mt) cc_final: 0.7437 (mt) REVERT: u 192 LYS cc_start: 0.8125 (tptp) cc_final: 0.7894 (mmmt) REVERT: v 11 VAL cc_start: 0.5205 (t) cc_final: 0.4607 (t) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2447 time to fit residues: 54.1744 Evaluate side-chains 125 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 30.0000 chunk 14 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.208626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.192917 restraints weight = 54471.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.194573 restraints weight = 38943.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.195844 restraints weight = 27901.988| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4482 r_free = 0.4482 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4482 r_free = 0.4482 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.9321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9909 Z= 0.254 Angle : 0.738 9.541 13410 Z= 0.381 Chirality : 0.044 0.215 1479 Planarity : 0.005 0.059 1735 Dihedral : 5.104 23.469 1346 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.41 % 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: -1.13 (0.24), residues: 1226 helix: 0.47 (0.19), residues: 751 sheet: -1.41 (0.52), residues: 81 loop : -3.04 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP v 141 HIS 0.009 0.002 HIS u 206 PHE 0.028 0.003 PHE t 718 TYR 0.034 0.002 TYR t 128 ARG 0.010 0.001 ARG t 246 ********************** 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 165 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.052 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: 0.5863 (m-30) cc_final: 0.5471 (m-30) REVERT: t 149 LYS cc_start: 0.8825 (tptp) cc_final: 0.8583 (tptp) REVERT: t 152 TRP cc_start: 0.7971 (t60) cc_final: 0.7532 (t60) REVERT: t 206 MET cc_start: 0.9310 (mtm) cc_final: 0.8700 (mtp) REVERT: t 314 ILE cc_start: 0.9127 (mt) cc_final: 0.8504 (mt) REVERT: t 375 ASP cc_start: 0.6419 (t70) cc_final: 0.6014 (t70) REVERT: t 441 LEU cc_start: 0.8999 (tp) cc_final: 0.8781 (tp) REVERT: t 580 MET cc_start: 0.0084 (tpp) cc_final: -0.0431 (tpp) REVERT: t 608 MET cc_start: 0.5929 (ttt) cc_final: 0.5584 (ttm) REVERT: t 694 ASP cc_start: 0.8203 (m-30) cc_final: 0.7862 (m-30) REVERT: t 705 MET cc_start: 0.8539 (ptt) cc_final: 0.7911 (ptt) REVERT: u 49 THR cc_start: 0.9221 (m) cc_final: 0.8925 (p) REVERT: u 162 LEU cc_start: 0.7823 (mt) cc_final: 0.7443 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2508 time to fit residues: 56.7594 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 : 1.047 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 136 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 = 0.5038 r_free = 0.5038 target = 0.211178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.195874 restraints weight = 54025.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.197571 restraints weight = 37422.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.198817 restraints weight = 27092.505| |-----------------------------------------------------------------------------| r_work (final): 0.4591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.9405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 9909 Z= 0.218 Angle : 0.716 13.100 13410 Z= 0.361 Chirality : 0.043 0.257 1479 Planarity : 0.005 0.072 1735 Dihedral : 4.913 22.089 1346 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.34 % Favored : 92.58 % 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: -0.91 (0.24), residues: 1226 helix: 0.68 (0.19), residues: 753 sheet: -1.35 (0.54), residues: 81 loop : -3.02 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP v 141 HIS 0.006 0.001 HIS u 206 PHE 0.025 0.002 PHE t 718 TYR 0.048 0.002 TYR t 700 ARG 0.008 0.001 ARG t 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.52 seconds wall clock time: 54 minutes 43.71 seconds (3283.71 seconds total)