Starting phenix.real_space_refine on Sat Aug 23 23:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6v_18199/08_2025/8q6v_18199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6v_18199/08_2025/8q6v_18199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q6v_18199/08_2025/8q6v_18199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6v_18199/08_2025/8q6v_18199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q6v_18199/08_2025/8q6v_18199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6v_18199/08_2025/8q6v_18199.map" } resolution = 3.23 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= 0.015 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 29 5.16 5 C 5100 2.51 5 N 1341 2.21 5 O 1438 1.98 5 H 7497 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15406 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5714 Classifications: {'peptide': 370} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 9691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 9691 Classifications: {'peptide': 651} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 49, 'TRANS': 601} Chain breaks: 6 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 16, 'ASN:plan1': 7, 'ASP:plan': 11, 'HIS:plan': 2, 'GLN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 200 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.16 Number of scatterers: 15406 At special positions: 0 Unit cell: (71.724, 86.736, 131.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 Mg 1 11.99 O 1438 8.00 N 1341 7.00 C 5100 6.00 H 7497 1.00 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: 1.24 Conformation dependent library (CDL) restraints added in 405.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 47.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 79 through 92 removed outlier: 4.116A pdb=" N HIS A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.776A pdb=" N GLY A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.881A pdb=" N ILE A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.640A pdb=" N THR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.692A pdb=" N GLU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.940A pdb=" N ARG B 8 " --> pdb=" O PRO B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 72 through 92 Processing helix chain 'B' and resid 106 through 128 removed outlier: 3.988A pdb=" N GLN B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.529A pdb=" N THR B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 185 removed outlier: 4.090A pdb=" N ARG B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 235 through 244 removed outlier: 3.934A pdb=" N HIS B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.695A pdb=" N GLU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 373 through 398 removed outlier: 3.991A pdb=" N THR B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 614 removed outlier: 5.242A pdb=" N THR B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 645 removed outlier: 3.594A pdb=" N TYR B 642 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.592A pdb=" N PHE B 664 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 691 through 698 removed outlier: 4.438A pdb=" N HIS B 696 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.857A pdb=" N ARG B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 742 through 752 Processing helix chain 'B' and resid 753 through 757 Processing helix chain 'B' and resid 758 through 763 Processing helix chain 'B' and resid 780 through 789 Processing helix chain 'B' and resid 838 through 842 Processing helix chain 'B' and resid 873 through 882 Processing helix chain 'B' and resid 920 through 928 removed outlier: 3.811A pdb=" N PHE B 925 " --> pdb=" O TYR B 921 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 926 " --> pdb=" O ARG B 922 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 4.803A pdb=" N PHE A 104 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLU A 139 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 101 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY A 219 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 103 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU A 221 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 25 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 208 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU A 23 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.806A pdb=" N ASN A 44 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS A 224 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 275 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 279 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 276 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU A 292 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 290 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 280 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.665A pdb=" N HIS B 227 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 251 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 229 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS B 228 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 49 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR B 230 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR B 51 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU B 47 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 96 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN B 49 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 98 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR B 51 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN B 192 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 95 " --> pdb=" O GLN B 192 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 194 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 97 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 193 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 771 " --> pdb=" O TYR B 848 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 723 through 724 343 hydrogen bonds defined for protein. 939 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: 2.62 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 7483 1.12 - 1.30: 1312 1.30 - 1.47: 3183 1.47 - 1.65: 3585 1.65 - 1.82: 44 Bond restraints: 15607 Sorted by residual: bond pdb=" N ALA B 928 " pdb=" H ALA B 928 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LEU B 182 " pdb=" H LEU B 182 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA B 760 " pdb=" H ALA B 760 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL B 307 " pdb=" H VAL B 307 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ARG B 624 " pdb=" H ARG B 624 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 15602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 24635 2.84 - 5.68: 2725 5.68 - 8.52: 752 8.52 - 11.36: 6 11.36 - 14.21: 14 Bond angle restraints: 28132 Sorted by residual: angle pdb=" C GLY A 133 " pdb=" N GLN A 134 " pdb=" CA GLN A 134 " ideal model delta sigma weight residual 121.75 132.46 -10.71 1.73e+00 3.34e-01 3.84e+01 angle pdb=" C PHE B 600 " pdb=" N GLU B 601 " pdb=" CA GLU B 601 " ideal model delta sigma weight residual 120.58 127.24 -6.66 1.32e+00 5.74e-01 2.55e+01 angle pdb=" OE1 GLN B 913 " pdb=" CD GLN B 913 " pdb=" NE2 GLN B 913 " ideal model delta sigma weight residual 122.60 117.65 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" CB HIS B 337 " pdb=" CG HIS B 337 " pdb=" CD2 HIS B 337 " ideal model delta sigma weight residual 131.20 124.85 6.35 1.30e+00 5.92e-01 2.38e+01 angle pdb=" N VAL B 96 " pdb=" CA VAL B 96 " pdb=" C VAL B 96 " ideal model delta sigma weight residual 108.42 115.36 -6.94 1.43e+00 4.89e-01 2.36e+01 ... (remaining 28127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6845 17.69 - 35.38: 407 35.38 - 53.07: 105 53.07 - 70.76: 110 70.76 - 88.45: 7 Dihedral angle restraints: 7474 sinusoidal: 3874 harmonic: 3600 Sorted by residual: dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N ARG A 354 " pdb=" CA ARG A 354 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA PRO B 770 " pdb=" C PRO B 770 " pdb=" N VAL B 771 " pdb=" CA VAL B 771 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR B 364 " pdb=" C THR B 364 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 735 0.072 - 0.144: 372 0.144 - 0.216: 97 0.216 - 0.288: 14 0.288 - 0.360: 3 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CA HIS B 244 " pdb=" N HIS B 244 " pdb=" C HIS B 244 " pdb=" CB HIS B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA PRO B 836 " pdb=" N PRO B 836 " pdb=" C PRO B 836 " pdb=" CB PRO B 836 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA LYS B 845 " pdb=" N LYS B 845 " pdb=" C LYS B 845 " pdb=" CB LYS B 845 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1218 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 285 " 0.247 2.00e-02 2.50e+03 9.63e-02 2.78e+02 pdb=" CG TYR A 285 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 285 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 285 " -0.092 2.00e-02 2.50e+03 pdb=" CE1 TYR A 285 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 285 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 285 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 285 " 0.153 2.00e-02 2.50e+03 pdb=" HD1 TYR A 285 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR A 285 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR A 285 " -0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR A 285 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 803 " 0.144 2.00e-02 2.50e+03 1.35e-01 2.75e+02 pdb=" CD GLN B 803 " -0.049 2.00e-02 2.50e+03 pdb=" OE1 GLN B 803 " -0.088 2.00e-02 2.50e+03 pdb=" NE2 GLN B 803 " -0.122 2.00e-02 2.50e+03 pdb="HE21 GLN B 803 " -0.112 2.00e-02 2.50e+03 pdb="HE22 GLN B 803 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " -0.120 2.00e-02 2.50e+03 1.17e-01 2.04e+02 pdb=" CG ASN A 42 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " 0.117 2.00e-02 2.50e+03 pdb="HD21 ASN A 42 " 0.093 2.00e-02 2.50e+03 pdb="HD22 ASN A 42 " -0.195 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 980 2.20 - 2.80: 27098 2.80 - 3.40: 42155 3.40 - 4.00: 54827 4.00 - 4.60: 80294 Nonbonded interactions: 205354 Sorted by model distance: nonbonded pdb=" HH TYR B 657 " pdb=" OD2 ASP B 724 " model vdw 1.596 2.450 nonbonded pdb=" O ILE A 251 " pdb=" HG1 THR A 254 " model vdw 1.608 2.450 nonbonded pdb=" OD1 ASP A 58 " pdb=" HG SER A 60 " model vdw 1.617 2.450 nonbonded pdb=" OE2 GLU A 23 " pdb=" HG SER A 205 " model vdw 1.621 2.450 nonbonded pdb=" HH TYR B 221 " pdb=" OE1 GLU B 245 " model vdw 1.627 2.450 ... (remaining 205349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.970 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.012 0.044 8110 Z= 0.699 Angle : 1.713 10.714 11033 Z= 1.155 Chirality : 0.087 0.360 1221 Planarity : 0.015 0.124 1429 Dihedral : 13.171 88.451 2888 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.06 (0.25), residues: 1003 helix: -0.80 (0.23), residues: 381 sheet: -0.00 (0.46), residues: 114 loop : -0.67 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 86 TYR 0.215 0.022 TYR A 285 PHE 0.062 0.011 PHE A 344 TRP 0.113 0.022 TRP B 355 HIS 0.009 0.002 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.01181 ( 8110) covalent geometry : angle 1.71293 (11033) hydrogen bonds : bond 0.16837 ( 343) hydrogen bonds : angle 7.31462 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.349 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.5389 (mtt) cc_final: 0.5122 (mtp) REVERT: B 87 VAL cc_start: 0.9185 (t) cc_final: 0.8704 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1773 time to fit residues: 37.4444 Evaluate side-chains 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN B 192 GLN B 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057399 restraints weight = 78146.628| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.04 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8110 Z= 0.142 Angle : 0.648 6.107 11033 Z= 0.350 Chirality : 0.043 0.155 1221 Planarity : 0.004 0.035 1429 Dihedral : 6.374 68.199 1104 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.87 % Allowed : 7.22 % Favored : 91.91 % 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: -0.03 (0.26), residues: 1003 helix: 0.61 (0.25), residues: 388 sheet: -0.51 (0.41), residues: 128 loop : -0.27 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 318 TYR 0.023 0.002 TYR A 285 PHE 0.020 0.002 PHE A 344 TRP 0.017 0.002 TRP B 355 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8110) covalent geometry : angle 0.64809 (11033) hydrogen bonds : bond 0.05251 ( 343) hydrogen bonds : angle 5.50723 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.9386 (tt0) cc_final: 0.8753 (tp-100) REVERT: B 54 MET cc_start: 0.9565 (tpt) cc_final: 0.9341 (tpp) REVERT: B 349 ASP cc_start: 0.9410 (p0) cc_final: 0.9185 (p0) REVERT: B 842 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9009 (mp) REVERT: B 912 THR cc_start: 0.9353 (m) cc_final: 0.8852 (t) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.1792 time to fit residues: 24.9298 Evaluate side-chains 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 268 CYS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.071584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055950 restraints weight = 80673.280| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.13 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8110 Z= 0.145 Angle : 0.563 5.409 11033 Z= 0.299 Chirality : 0.041 0.149 1221 Planarity : 0.004 0.042 1429 Dihedral : 5.699 66.393 1104 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.75 % Allowed : 8.72 % Favored : 90.54 % 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: 0.43 (0.27), residues: 1003 helix: 1.25 (0.26), residues: 388 sheet: -0.50 (0.40), residues: 129 loop : -0.18 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 127 TYR 0.020 0.001 TYR A 285 PHE 0.020 0.001 PHE A 131 TRP 0.013 0.002 TRP B 291 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8110) covalent geometry : angle 0.56319 (11033) hydrogen bonds : bond 0.04354 ( 343) hydrogen bonds : angle 5.05501 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.360 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: A 267 GLN cc_start: 0.9417 (tt0) cc_final: 0.8662 (tp-100) REVERT: B 76 MET cc_start: 0.8773 (mtp) cc_final: 0.8448 (mtt) REVERT: B 912 THR cc_start: 0.9406 (m) cc_final: 0.8948 (t) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.1418 time to fit residues: 16.5911 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4998 > 50: distance: 36 - 48: 35.186 distance: 48 - 49: 18.319 distance: 48 - 53: 10.612 distance: 49 - 50: 16.377 distance: 49 - 52: 22.248 distance: 49 - 54: 43.864 distance: 50 - 55: 43.253 distance: 55 - 56: 35.731 distance: 55 - 60: 33.284 distance: 56 - 57: 34.937 distance: 56 - 59: 32.516 distance: 56 - 61: 11.346 distance: 57 - 58: 16.696 distance: 57 - 65: 31.291 distance: 59 - 62: 32.222 distance: 59 - 63: 21.247 distance: 59 - 64: 27.194 distance: 65 - 66: 19.880 distance: 65 - 71: 50.292 distance: 66 - 69: 56.686 distance: 66 - 72: 40.166 distance: 67 - 68: 67.532 distance: 67 - 76: 49.575 distance: 69 - 70: 40.956 distance: 69 - 74: 39.613 distance: 70 - 75: 40.402 distance: 76 - 77: 30.701 distance: 76 - 81: 23.899 distance: 77 - 78: 30.363 distance: 77 - 80: 40.339 distance: 77 - 82: 43.424 distance: 78 - 79: 35.074 distance: 78 - 83: 36.800 distance: 83 - 84: 53.040 distance: 83 - 89: 23.316 distance: 84 - 85: 53.367 distance: 84 - 87: 58.909 distance: 84 - 90: 50.607 distance: 85 - 86: 28.596 distance: 85 - 97: 45.992 distance: 87 - 88: 36.026 distance: 87 - 91: 24.842 distance: 87 - 92: 34.421 distance: 88 - 89: 22.225 distance: 88 - 93: 7.606 distance: 88 - 94: 24.211 distance: 89 - 95: 19.476 distance: 89 - 96: 17.852 distance: 97 - 98: 5.004 distance: 97 - 102: 40.004 distance: 98 - 99: 40.624 distance: 98 - 101: 49.616 distance: 98 - 103: 6.351 distance: 99 - 100: 40.069 distance: 99 - 104: 17.592 distance: 104 - 105: 22.126 distance: 104 - 108: 40.450 distance: 105 - 106: 22.830 distance: 105 - 109: 26.456 distance: 105 - 110: 23.492 distance: 106 - 107: 23.740 distance: 106 - 111: 14.616 distance: 111 - 112: 15.564 distance: 111 - 120: 29.152 distance: 112 - 113: 12.226 distance: 112 - 115: 48.087 distance: 112 - 121: 45.476 distance: 113 - 126: 6.646 distance: 115 - 116: 12.091 distance: 115 - 122: 29.667 distance: 115 - 123: 41.686 distance: 116 - 117: 15.961 distance: 116 - 125: 41.038 distance: 117 - 118: 18.290 distance: 117 - 119: 17.362 distance: 126 - 127: 24.263 distance: 126 - 134: 36.287 distance: 127 - 128: 55.247 distance: 127 - 130: 9.430 distance: 127 - 135: 57.085 distance: 128 - 129: 25.141 distance: 128 - 145: 10.340 distance: 130 - 131: 30.413 distance: 130 - 136: 42.664 distance: 130 - 137: 20.183 distance: 131 - 133: 45.323 distance: 131 - 138: 17.153 distance: 132 - 139: 9.657 distance: 132 - 140: 13.459 distance: 133 - 142: 18.673 distance: 133 - 143: 45.378 distance: 133 - 144: 42.216 distance: 145 - 146: 22.625 distance: 145 - 153: 39.814 distance: 146 - 147: 9.639 distance: 146 - 149: 27.086 distance: 146 - 154: 20.470 distance: 147 - 148: 7.502 distance: 147 - 157: 21.747 distance: 149 - 150: 35.990 distance: 149 - 155: 5.712 distance: 149 - 156: 32.379 distance: 150 - 151: 11.291 distance: 150 - 152: 28.445