Starting phenix.real_space_refine on Wed Sep 17 16:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hd5_0201/09_2025/6hd5_0201_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hd5_0201/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6hd5_0201/09_2025/6hd5_0201_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hd5_0201/09_2025/6hd5_0201_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hd5_0201/09_2025/6hd5_0201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hd5_0201/09_2025/6hd5_0201.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 5} 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: {'ASP:plan': 8, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 4} 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: {'GLU:plan': 1, 'GLN:plan1': 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: 2.31, per 1000 atoms: 0.24 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: 0.96 Conformation dependent library (CDL) restraints added in 375.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.35 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: 1.55 Time building geometry restraints manager: 1.22 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 9909 Z= 0.089 Angle : 0.403 6.837 13410 Z= 0.249 Chirality : 0.034 0.125 1479 Planarity : 0.003 0.040 1735 Dihedral : 8.701 75.387 3626 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.52 % Favored : 88.42 % Rotamer: Outliers : 0.10 % Allowed : 1.01 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG u 142 TYR 0.012 0.001 TYR t 507 PHE 0.007 0.000 PHE t 800 TRP 0.006 0.001 TRP t 385 HIS 0.002 0.000 HIS t 576 Details of bonding type rmsd covalent geometry : bond 0.00139 ( 9909) covalent geometry : angle 0.40304 (13410) hydrogen bonds : bond 0.12643 ( 542) hydrogen bonds : angle 5.23447 ( 1679) *********************** 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 : 0.395 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: t 251 TYR cc_start: 0.4702 (m-10) cc_final: 0.4500 (m-80) REVERT: t 314 ILE cc_start: 0.7824 (mt) cc_final: 0.7220 (mt) REVERT: t 428 LEU cc_start: 0.8776 (mt) cc_final: 0.8541 (mt) REVERT: t 441 LEU cc_start: 0.7889 (tp) cc_final: 0.7192 (tp) REVERT: t 458 THR cc_start: 0.6485 (m) cc_final: 0.5832 (m) REVERT: t 543 ASN cc_start: 0.5120 (t0) cc_final: 0.4899 (t0) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.1320 time to fit residues: 54.6965 Evaluate side-chains 163 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 320 GLN t 347 ASN t 492 HIS t 735 ASN ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 153 HIS u 200 GLN v 32 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.200746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.173762 restraints weight = 36886.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.177691 restraints weight = 26980.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.180803 restraints weight = 20879.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.183286 restraints weight = 16751.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.185225 restraints weight = 13770.052| |-----------------------------------------------------------------------------| r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4746 r_free = 0.4746 target_work(ls_wunit_k1) = 0.187 | | 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) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 moved from start: 0.4163 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= 0.175 Angle : 0.644 8.418 13410 Z= 0.328 Chirality : 0.041 0.177 1479 Planarity : 0.004 0.060 1735 Dihedral : 3.484 22.911 1346 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.24), residues: 1226 helix: 1.05 (0.19), residues: 734 sheet: -0.68 (0.58), residues: 79 loop : -3.09 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG t 606 TYR 0.023 0.002 TYR t 421 PHE 0.018 0.002 PHE v 114 TRP 0.023 0.003 TRP t 162 HIS 0.006 0.001 HIS t 757 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9909) covalent geometry : angle 0.64351 (13410) hydrogen bonds : bond 0.03537 ( 542) hydrogen bonds : angle 3.96322 ( 1679) *********************** 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 : 0.400 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: t 34 LYS cc_start: 0.8722 (tptp) cc_final: 0.8465 (tppt) REVERT: t 206 MET cc_start: 0.9009 (mtm) cc_final: 0.8704 (mtt) REVERT: t 314 ILE cc_start: 0.9050 (mt) cc_final: 0.8612 (mt) REVERT: t 441 LEU cc_start: 0.8655 (tp) cc_final: 0.8157 (tp) REVERT: t 458 THR cc_start: 0.6565 (m) cc_final: 0.6173 (m) REVERT: t 567 GLN cc_start: 0.9190 (pt0) cc_final: 0.8661 (mm-40) REVERT: t 593 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7948 (pp20) REVERT: t 694 ASP cc_start: 0.7421 (m-30) cc_final: 0.7106 (m-30) REVERT: u 16 MET cc_start: 0.6712 (mtm) cc_final: 0.6362 (mtm) REVERT: u 162 LEU cc_start: 0.7228 (mt) cc_final: 0.6976 (mt) REVERT: v 147 PHE cc_start: 0.9173 (m-80) cc_final: 0.8897 (m-10) REVERT: v 172 LYS cc_start: 0.6817 (pttt) cc_final: 0.6421 (mmtt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1087 time to fit residues: 31.1517 Evaluate side-chains 147 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 112 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 = 0.5246 r_free = 0.5246 target = 0.241066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.224418 restraints weight = 54085.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5283 r_free = 0.5283 target = 0.226124 restraints weight = 38186.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.227362 restraints weight = 27968.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5311 r_free = 0.5311 target = 0.228280 restraints weight = 21121.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5319 r_free = 0.5319 target = 0.228981 restraints weight = 16410.085| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 moved from start: 0.4724 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= 0.115 Angle : 0.557 7.912 13410 Z= 0.282 Chirality : 0.038 0.123 1479 Planarity : 0.004 0.043 1735 Dihedral : 3.345 25.339 1346 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.24), residues: 1226 helix: 1.32 (0.19), residues: 744 sheet: -0.45 (0.58), residues: 81 loop : -2.96 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG u 159 TYR 0.046 0.001 TYR t 550 PHE 0.017 0.002 PHE t 681 TRP 0.016 0.002 TRP t 113 HIS 0.007 0.001 HIS u 145 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9909) covalent geometry : angle 0.55689 (13410) hydrogen bonds : bond 0.02899 ( 542) hydrogen bonds : angle 3.61409 ( 1679) *********************** 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 193 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.384 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 152 TRP cc_start: 0.7945 (t60) cc_final: 0.7624 (t-100) REVERT: t 206 MET cc_start: 0.9002 (mtm) cc_final: 0.8715 (mtm) REVERT: t 314 ILE cc_start: 0.8962 (mt) cc_final: 0.8377 (mt) REVERT: t 441 LEU cc_start: 0.8860 (tp) cc_final: 0.8423 (tp) REVERT: t 458 THR cc_start: 0.6550 (m) cc_final: 0.6286 (m) REVERT: t 567 GLN cc_start: 0.9205 (pt0) cc_final: 0.8751 (mm-40) REVERT: t 694 ASP cc_start: 0.7270 (m-30) cc_final: 0.6966 (m-30) REVERT: u 10 ILE cc_start: 0.1884 (tt) cc_final: 0.1518 (mt) REVERT: u 16 MET cc_start: 0.6706 (mtm) cc_final: 0.6425 (mtm) REVERT: u 95 TYR cc_start: 0.4183 (p90) cc_final: 0.3918 (p90) REVERT: u 162 LEU cc_start: 0.7485 (mt) cc_final: 0.7227 (mt) REVERT: v 57 ASP cc_start: 0.6430 (m-30) cc_final: 0.6218 (t0) REVERT: v 65 TYR cc_start: 0.7711 (m-80) cc_final: 0.6851 (m-80) REVERT: v 147 PHE cc_start: 0.8998 (m-80) cc_final: 0.8744 (m-10) REVERT: v 172 LYS cc_start: 0.6470 (pttt) cc_final: 0.5949 (mttm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1026 time to fit residues: 27.9938 Evaluate side-chains 150 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 54 optimal weight: 8.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** t 219 ASN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 619 HIS ** u 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.193187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.168196 restraints weight = 35728.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.172797 restraints weight = 24261.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.176327 restraints weight = 17530.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.179174 restraints weight = 13240.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.181323 restraints weight = 10263.596| |-----------------------------------------------------------------------------| r_work (final): 0.4655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.5431 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= 0.137 Angle : 0.603 8.688 13410 Z= 0.308 Chirality : 0.039 0.161 1479 Planarity : 0.004 0.061 1735 Dihedral : 3.640 24.915 1346 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.78 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1226 helix: 1.27 (0.19), residues: 755 sheet: -0.55 (0.56), residues: 81 loop : -2.88 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 148 TYR 0.029 0.002 TYR t 550 PHE 0.023 0.002 PHE t 275 TRP 0.012 0.002 TRP u 40 HIS 0.007 0.001 HIS t 619 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9909) covalent geometry : angle 0.60261 (13410) hydrogen bonds : bond 0.03043 ( 542) hydrogen bonds : angle 3.72570 ( 1679) *********************** 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 190 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.394 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: t 97 LEU cc_start: 0.9060 (mt) cc_final: 0.8710 (mt) REVERT: t 140 ASP cc_start: 0.5508 (t0) cc_final: 0.5267 (t0) REVERT: t 206 MET cc_start: 0.9179 (mtm) cc_final: 0.8682 (mtm) REVERT: t 314 ILE cc_start: 0.9101 (mt) cc_final: 0.8590 (mt) REVERT: t 441 LEU cc_start: 0.8922 (tp) cc_final: 0.8517 (tp) REVERT: t 458 THR cc_start: 0.6930 (m) cc_final: 0.6705 (m) REVERT: t 567 GLN cc_start: 0.9305 (pt0) cc_final: 0.8793 (mm-40) REVERT: t 694 ASP cc_start: 0.7433 (m-30) cc_final: 0.7110 (m-30) REVERT: u 16 MET cc_start: 0.6244 (mtm) cc_final: 0.6029 (mtm) REVERT: u 95 TYR cc_start: 0.4499 (p90) cc_final: 0.4236 (p90) REVERT: u 162 LEU cc_start: 0.7435 (mt) cc_final: 0.7140 (mt) REVERT: u 225 LEU cc_start: 0.8832 (mt) cc_final: 0.8617 (mt) REVERT: v 57 ASP cc_start: 0.6701 (m-30) cc_final: 0.6278 (t0) REVERT: v 172 LYS cc_start: 0.6681 (pttt) cc_final: 0.6141 (mttm) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.0990 time to fit residues: 26.6241 Evaluate side-chains 146 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 119 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 137 GLN t 161 ASN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 172 ASN t 219 ASN t 481 ASN t 544 GLN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 676 GLN u 112 ASN ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.185387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.162808 restraints weight = 39892.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.167019 restraints weight = 26712.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.170252 restraints weight = 19212.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.172681 restraints weight = 14320.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.174638 restraints weight = 11093.890| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4590 r_free = 0.4590 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4590 r_free = 0.4590 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9909 Z= 0.189 Angle : 0.712 8.102 13410 Z= 0.366 Chirality : 0.040 0.138 1479 Planarity : 0.005 0.048 1735 Dihedral : 4.314 23.008 1346 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 0.20 % Allowed : 2.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.23), residues: 1226 helix: 0.82 (0.19), residues: 748 sheet: -0.69 (0.57), residues: 79 loop : -2.81 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG t 246 TYR 0.032 0.002 TYR t 550 PHE 0.030 0.003 PHE u 139 TRP 0.028 0.004 TRP t 162 HIS 0.010 0.002 HIS t 53 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9909) covalent geometry : angle 0.71165 (13410) hydrogen bonds : bond 0.03916 ( 542) hydrogen bonds : angle 4.21657 ( 1679) *********************** 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 184 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.436 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: 0.5638 (m-30) cc_final: 0.5373 (m-30) REVERT: t 158 TYR cc_start: 0.7788 (t80) cc_final: 0.6369 (m-80) REVERT: t 206 MET cc_start: 0.9239 (mtm) cc_final: 0.8721 (mtm) REVERT: t 314 ILE cc_start: 0.9040 (mt) cc_final: 0.8474 (mt) REVERT: t 428 LEU cc_start: 0.9118 (mt) cc_final: 0.8797 (mt) REVERT: t 434 MET cc_start: 0.8909 (mtt) cc_final: 0.8274 (mmt) REVERT: t 690 THR cc_start: 0.8636 (p) cc_final: 0.8388 (p) REVERT: t 694 ASP cc_start: 0.7794 (m-30) cc_final: 0.7465 (m-30) REVERT: u 29 MET cc_start: 0.3709 (mmt) cc_final: 0.3497 (mmt) REVERT: u 127 MET cc_start: 0.1133 (mtt) cc_final: 0.0738 (mtt) REVERT: u 162 LEU cc_start: 0.7574 (mt) cc_final: 0.7296 (mt) REVERT: u 225 LEU cc_start: 0.9009 (mt) cc_final: 0.8775 (mt) REVERT: v 57 ASP cc_start: 0.6388 (m-30) cc_final: 0.5806 (t0) REVERT: v 102 TYR cc_start: 0.4192 (m-80) cc_final: 0.3984 (m-80) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.0988 time to fit residues: 25.6599 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 112 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 430 HIS ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 617 GLN u 132 ASN u 136 GLN ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.226591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.210457 restraints weight = 54603.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.212201 restraints weight = 38442.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.213481 restraints weight = 27896.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.214441 restraints weight = 20798.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.215124 restraints weight = 15930.043| |-----------------------------------------------------------------------------| r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9909 Z= 0.134 Angle : 0.627 11.778 13410 Z= 0.318 Chirality : 0.039 0.161 1479 Planarity : 0.004 0.047 1735 Dihedral : 4.110 22.914 1346 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.24), residues: 1226 helix: 0.94 (0.19), residues: 750 sheet: -0.55 (0.56), residues: 81 loop : -2.79 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 246 TYR 0.025 0.002 TYR t 550 PHE 0.033 0.002 PHE u 45 TRP 0.026 0.002 TRP t 162 HIS 0.004 0.001 HIS t 430 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9909) covalent geometry : angle 0.62721 (13410) hydrogen bonds : bond 0.03327 ( 542) hydrogen bonds : angle 4.05224 ( 1679) *********************** 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 179 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.441 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: t 97 LEU cc_start: 0.9131 (mt) cc_final: 0.8851 (mt) REVERT: t 152 TRP cc_start: 0.7884 (t60) cc_final: 0.7539 (t60) REVERT: t 158 TYR cc_start: 0.8411 (t80) cc_final: 0.6741 (m-80) REVERT: t 206 MET cc_start: 0.9313 (mtm) cc_final: 0.8477 (mtm) REVERT: t 314 ILE cc_start: 0.9026 (mt) cc_final: 0.8422 (mt) REVERT: t 441 LEU cc_start: 0.8986 (tp) cc_final: 0.8680 (tp) REVERT: t 567 GLN cc_start: 0.9202 (pt0) cc_final: 0.8308 (mm-40) REVERT: t 690 THR cc_start: 0.8632 (p) cc_final: 0.8416 (p) REVERT: t 694 ASP cc_start: 0.7640 (m-30) cc_final: 0.7323 (m-30) REVERT: u 29 MET cc_start: 0.3385 (mmt) cc_final: 0.3173 (mmt) REVERT: u 49 THR cc_start: 0.8986 (m) cc_final: 0.8744 (p) REVERT: u 127 MET cc_start: 0.1323 (mtt) cc_final: 0.0880 (mtt) REVERT: u 155 ARG cc_start: 0.7266 (mtt-85) cc_final: 0.6658 (mtt-85) REVERT: u 162 LEU cc_start: 0.7769 (mt) cc_final: 0.7452 (mt) REVERT: u 225 LEU cc_start: 0.8906 (mt) cc_final: 0.8692 (mt) REVERT: v 57 ASP cc_start: 0.6225 (m-30) cc_final: 0.5690 (t0) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1064 time to fit residues: 26.4202 Evaluate side-chains 140 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 137 GLN ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 617 GLN u 136 GLN ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 153 HIS u 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.214187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.198577 restraints weight = 54412.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.200316 restraints weight = 38129.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.201636 restraints weight = 26133.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.202625 restraints weight = 19606.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.203376 restraints weight = 14630.395| |-----------------------------------------------------------------------------| r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4563 r_free = 0.4563 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4563 r_free = 0.4563 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.7931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9909 Z= 0.209 Angle : 0.774 8.498 13410 Z= 0.403 Chirality : 0.044 0.278 1479 Planarity : 0.005 0.054 1735 Dihedral : 4.911 22.020 1346 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.23), residues: 1226 helix: 0.27 (0.18), residues: 755 sheet: -0.57 (0.64), residues: 61 loop : -2.96 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 557 TYR 0.026 0.003 TYR t 550 PHE 0.036 0.003 PHE u 45 TRP 0.025 0.003 TRP v 141 HIS 0.008 0.002 HIS u 206 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9909) covalent geometry : angle 0.77420 (13410) hydrogen bonds : bond 0.04507 ( 542) hydrogen bonds : angle 4.65396 ( 1679) *********************** 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 180 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 22 ASP cc_start: 0.5743 (m-30) cc_final: 0.5441 (m-30) REVERT: t 101 MET cc_start: 0.8311 (mtp) cc_final: 0.8029 (mtp) REVERT: t 152 TRP cc_start: 0.7787 (t60) cc_final: 0.7487 (t60) REVERT: t 158 TYR cc_start: 0.8237 (t80) cc_final: 0.6424 (m-80) REVERT: t 206 MET cc_start: 0.9410 (mtm) cc_final: 0.8735 (mtp) REVERT: t 375 ASP cc_start: 0.7029 (t70) cc_final: 0.6576 (t70) REVERT: t 441 LEU cc_start: 0.9031 (tp) cc_final: 0.8802 (tp) REVERT: t 608 MET cc_start: 0.5870 (ttt) cc_final: 0.5260 (ttt) REVERT: t 703 TYR cc_start: 0.8436 (t80) cc_final: 0.8094 (t80) REVERT: u 29 MET cc_start: 0.3614 (mmt) cc_final: 0.3275 (tpp) REVERT: u 121 MET cc_start: 0.2295 (tpt) cc_final: 0.2071 (tpt) REVERT: u 127 MET cc_start: 0.1169 (mtt) cc_final: 0.0909 (mtt) REVERT: u 162 LEU cc_start: 0.7764 (mt) cc_final: 0.7491 (mt) REVERT: u 225 LEU cc_start: 0.8876 (mt) cc_final: 0.8668 (mt) REVERT: v 57 ASP cc_start: 0.6437 (m-30) cc_final: 0.5658 (t0) REVERT: v 147 PHE cc_start: 0.9117 (m-10) cc_final: 0.8757 (m-10) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1082 time to fit residues: 27.0778 Evaluate side-chains 136 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 0.0270 chunk 105 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 101 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 = 0.5082 r_free = 0.5082 target = 0.216606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.200538 restraints weight = 54002.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.202324 restraints weight = 37789.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.203598 restraints weight = 27257.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.204525 restraints weight = 20422.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.205208 restraints weight = 15710.318| |-----------------------------------------------------------------------------| r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4653 r_free = 0.4653 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9909 Z= 0.156 Angle : 0.706 9.913 13410 Z= 0.359 Chirality : 0.042 0.158 1479 Planarity : 0.005 0.049 1735 Dihedral : 4.719 22.516 1346 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.20 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.23), residues: 1226 helix: 0.52 (0.18), residues: 751 sheet: -0.63 (0.63), residues: 66 loop : -2.87 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 246 TYR 0.029 0.002 TYR t 817 PHE 0.039 0.002 PHE u 45 TRP 0.029 0.002 TRP t 162 HIS 0.006 0.001 HIS t 430 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9909) covalent geometry : angle 0.70592 (13410) hydrogen bonds : bond 0.03770 ( 542) hydrogen bonds : angle 4.44720 ( 1679) *********************** 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 166 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.454 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: 0.5788 (m-30) cc_final: 0.5473 (m-30) REVERT: t 97 LEU cc_start: 0.8953 (mt) cc_final: 0.8545 (mt) REVERT: t 152 TRP cc_start: 0.7312 (t60) cc_final: 0.7009 (t60) REVERT: t 158 TYR cc_start: 0.7972 (t80) cc_final: 0.6428 (m-80) REVERT: t 206 MET cc_start: 0.9445 (mtm) cc_final: 0.8792 (mtp) REVERT: t 375 ASP cc_start: 0.6920 (t70) cc_final: 0.6481 (t70) REVERT: t 608 MET cc_start: 0.5994 (ttt) cc_final: 0.5276 (ttm) REVERT: u 29 MET cc_start: 0.3147 (mmt) cc_final: 0.2781 (tpp) REVERT: u 162 LEU cc_start: 0.7772 (mt) cc_final: 0.7463 (mt) REVERT: v 102 TYR cc_start: 0.4371 (m-80) cc_final: 0.4101 (m-80) REVERT: v 147 PHE cc_start: 0.9133 (m-10) cc_final: 0.8893 (m-10) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1037 time to fit residues: 24.2792 Evaluate side-chains 126 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 19 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 101 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 = 0.5071 r_free = 0.5071 target = 0.215233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.199147 restraints weight = 53914.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.200883 restraints weight = 37370.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.202145 restraints weight = 26881.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.203043 restraints weight = 20027.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.203679 restraints weight = 15442.879| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4638 r_free = 0.4638 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4638 r_free = 0.4638 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.8423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9909 Z= 0.154 Angle : 0.697 9.167 13410 Z= 0.357 Chirality : 0.043 0.181 1479 Planarity : 0.005 0.058 1735 Dihedral : 4.720 21.979 1346 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.23), residues: 1226 helix: 0.57 (0.18), residues: 744 sheet: -0.67 (0.64), residues: 60 loop : -2.78 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG t 246 TYR 0.034 0.002 TYR t 128 PHE 0.034 0.002 PHE u 45 TRP 0.022 0.002 TRP t 162 HIS 0.006 0.001 HIS u 206 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9909) covalent geometry : angle 0.69657 (13410) hydrogen bonds : bond 0.03788 ( 542) hydrogen bonds : angle 4.45363 ( 1679) *********************** 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 : 0.403 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: 0.5873 (m-30) cc_final: 0.5496 (m-30) REVERT: t 152 TRP cc_start: 0.7428 (t60) cc_final: 0.7075 (t60) REVERT: t 206 MET cc_start: 0.9490 (mtm) cc_final: 0.8960 (mtp) REVERT: t 314 ILE cc_start: 0.9123 (mt) cc_final: 0.8495 (mt) REVERT: t 375 ASP cc_start: 0.6944 (t70) cc_final: 0.6510 (t70) REVERT: t 580 MET cc_start: 0.0451 (tpp) cc_final: 0.0237 (tpp) REVERT: t 608 MET cc_start: 0.5872 (ttt) cc_final: 0.5437 (ttm) REVERT: u 29 MET cc_start: 0.3096 (mmt) cc_final: 0.2747 (tpp) REVERT: u 162 LEU cc_start: 0.7847 (mt) cc_final: 0.7574 (mt) REVERT: v 57 ASP cc_start: 0.6863 (m-30) cc_final: 0.6110 (t0) REVERT: v 147 PHE cc_start: 0.9144 (m-10) cc_final: 0.8896 (m-10) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1056 time to fit residues: 24.1416 Evaluate side-chains 119 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 1.9990 chunk 92 optimal weight: 40.0000 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 229 HIS t 320 GLN t 392 GLN ** t 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** 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** ** v 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.220111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.203954 restraints weight = 53983.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.205691 restraints weight = 37562.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.206652 restraints weight = 26947.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.207693 restraints weight = 21200.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.208401 restraints weight = 16230.631| |-----------------------------------------------------------------------------| r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4595 r_free = 0.4595 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4595 r_free = 0.4595 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9909 Z= 0.129 Angle : 0.685 9.300 13410 Z= 0.346 Chirality : 0.042 0.193 1479 Planarity : 0.004 0.047 1735 Dihedral : 4.497 21.570 1346 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.24), residues: 1226 helix: 0.79 (0.19), residues: 744 sheet: -0.73 (0.59), residues: 75 loop : -2.68 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG t 246 TYR 0.038 0.002 TYR t 700 PHE 0.029 0.002 PHE t 718 TRP 0.017 0.002 TRP t 162 HIS 0.004 0.001 HIS u 206 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9909) covalent geometry : angle 0.68527 (13410) hydrogen bonds : bond 0.03497 ( 542) hydrogen bonds : angle 4.27644 ( 1679) ********************** 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 160 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 34 LYS cc_start: 0.8943 (tppt) cc_final: 0.8722 (tppt) REVERT: t 97 LEU cc_start: 0.8794 (mt) cc_final: 0.8555 (mt) REVERT: t 152 TRP cc_start: 0.7490 (t60) cc_final: 0.7173 (t60) REVERT: t 158 TYR cc_start: 0.8149 (t80) cc_final: 0.6244 (m-80) REVERT: t 206 MET cc_start: 0.9520 (mtm) cc_final: 0.8930 (mtp) REVERT: t 212 MET cc_start: 0.7770 (tpt) cc_final: 0.7382 (ttm) REVERT: t 314 ILE cc_start: 0.9095 (mt) cc_final: 0.8481 (mt) REVERT: t 375 ASP cc_start: 0.6981 (t70) cc_final: 0.6596 (t70) REVERT: t 567 GLN cc_start: 0.9091 (pt0) cc_final: 0.8140 (mm-40) REVERT: t 580 MET cc_start: 0.0339 (tpp) cc_final: -0.1336 (tpp) REVERT: t 608 MET cc_start: 0.5543 (ttt) cc_final: 0.5160 (ttm) REVERT: u 29 MET cc_start: 0.2669 (mmt) cc_final: 0.2335 (tpp) REVERT: u 115 ILE cc_start: 0.8436 (mm) cc_final: 0.8186 (mp) REVERT: u 127 MET cc_start: 0.0271 (mtt) cc_final: -0.0260 (mpp) REVERT: u 162 LEU cc_start: 0.7764 (mt) cc_final: 0.7493 (mt) REVERT: u 225 LEU cc_start: 0.8803 (mt) cc_final: 0.8601 (mt) REVERT: v 57 ASP cc_start: 0.6877 (m-30) cc_final: 0.6021 (t0) REVERT: v 147 PHE cc_start: 0.9122 (m-10) cc_final: 0.8861 (m-10) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1051 time to fit residues: 23.6585 Evaluate side-chains 129 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 chunk 119 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 572 GLN ** 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** ** v 101 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 = 0.5060 r_free = 0.5060 target = 0.213945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.197889 restraints weight = 54258.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.199581 restraints weight = 38269.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.200558 restraints weight = 27744.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.201610 restraints weight = 21961.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.202315 restraints weight = 16771.381| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4549 r_free = 0.4549 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4549 r_free = 0.4549 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5702 moved from start: 0.8865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9909 Z= 0.161 Angle : 0.709 8.068 13410 Z= 0.364 Chirality : 0.043 0.162 1479 Planarity : 0.005 0.050 1735 Dihedral : 4.680 20.253 1346 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1226 helix: 0.74 (0.19), residues: 742 sheet: -0.78 (0.59), residues: 75 loop : -2.73 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG t 606 TYR 0.037 0.002 TYR t 128 PHE 0.025 0.002 PHE u 45 TRP 0.019 0.002 TRP t 152 HIS 0.009 0.002 HIS u 145 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9909) covalent geometry : angle 0.70935 (13410) hydrogen bonds : bond 0.03752 ( 542) hydrogen bonds : angle 4.44224 ( 1679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1715.32 seconds wall clock time: 30 minutes 36.32 seconds (1836.32 seconds total)