Starting phenix.real_space_refine on Fri Jul 3 11:07:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osk_17157/07_2026/8osk_17157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osk_17157/07_2026/8osk_17157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8osk_17157/07_2026/8osk_17157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osk_17157/07_2026/8osk_17157.map" model { file = "/net/cci-nas-00/data/ceres_data/8osk_17157/07_2026/8osk_17157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osk_17157/07_2026/8osk_17157.cif" } resolution = 3.6 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= -0.004 sd= 0.951 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: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 14 5.16 5 C 7941 2.51 5 N 2662 2.21 5 O 3130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13995 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2520 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2564 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1591 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 1068 Unresolved non-hydrogen angles: 1365 Unresolved non-hydrogen dihedrals: 909 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'ASP:plan': 15, 'ARG:plan': 15, 'ASN:plan1': 10, 'GLU:plan': 28, 'GLN:plan1': 12, 'PHE:plan': 18, 'HIS:plan': 13, 'TYR:plan': 16, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 631 Chain: "N" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1427 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 4 Unresolved non-hydrogen bonds: 915 Unresolved non-hydrogen angles: 1154 Unresolved non-hydrogen dihedrals: 771 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'ARG:plan': 22, 'GLU:plan': 14, 'HIS:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 15, 'ASN:plan1': 10, 'PHE:plan': 16, 'TYR:plan': 9, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 517 Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 13995 At special positions: 0 Unit cell: (142.805, 145.34, 122.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 248 15.00 O 3130 8.00 N 2662 7.00 C 7941 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: 1.13 Conformation dependent library (CDL) restraints added in 512.7 milliseconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 60.6% alpha, 14.7% beta 124 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'M' and resid 34 through 60 removed outlier: 3.873A pdb=" N MET M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 90 Processing helix chain 'M' and resid 108 through 118 Processing helix chain 'M' and resid 136 through 143 removed outlier: 4.123A pdb=" N SER M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 150 Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 159 through 161 No H-bonds generated for 'chain 'M' and resid 159 through 161' Processing helix chain 'M' and resid 162 through 173 removed outlier: 3.568A pdb=" N VAL M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS M 173 " --> pdb=" O ILE M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 186 Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'M' and resid 300 through 305 removed outlier: 3.531A pdb=" N VAL M 304 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 313 Processing helix chain 'M' and resid 316 through 332 removed outlier: 4.156A pdb=" N ASN M 320 " --> pdb=" O ASP M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 384 removed outlier: 3.675A pdb=" N GLU M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 105 removed outlier: 3.663A pdb=" N LEU N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 112 Processing helix chain 'N' and resid 117 through 129 Processing helix chain 'N' and resid 151 through 160 Processing helix chain 'N' and resid 182 through 187 removed outlier: 3.519A pdb=" N ILE N 186 " --> pdb=" O SER N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 195 Processing helix chain 'N' and resid 198 through 202 Processing helix chain 'N' and resid 204 through 215 removed outlier: 4.228A pdb=" N ALA N 209 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS N 210 " --> pdb=" O LYS N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 249 No H-bonds generated for 'chain 'N' and resid 247 through 249' Processing helix chain 'N' and resid 360 through 368 removed outlier: 3.601A pdb=" N THR N 364 " --> pdb=" O ASP N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 375 Processing helix chain 'N' and resid 378 through 382 Processing helix chain 'N' and resid 384 through 399 removed outlier: 4.237A pdb=" N GLY N 389 " --> pdb=" O GLN N 385 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS N 390 " --> pdb=" O ASP N 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.006A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.214A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.886A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.398A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 131 through 134 removed outlier: 6.299A pdb=" N ILE M 131 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET M 126 " --> pdb=" O ILE M 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 264 through 266 removed outlier: 4.105A pdb=" N TRP M 350 " --> pdb=" O MET M 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 286 through 289 removed outlier: 6.129A pdb=" N ARG M 279 " --> pdb=" O LEU M 287 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU M 289 " --> pdb=" O THR M 277 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR M 277 " --> pdb=" O LEU M 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 176 through 179 removed outlier: 6.440A pdb=" N VAL N 168 " --> pdb=" O LEU N 177 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL N 179 " --> pdb=" O LEU N 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU N 166 " --> pdb=" O VAL N 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 356 through 359 removed outlier: 6.523A pdb=" N ARG N 349 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL N 359 " --> pdb=" O VAL N 347 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL N 347 " --> pdb=" O VAL N 359 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR N 439 " --> pdb=" O PHE N 429 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 356 through 359 removed outlier: 6.523A pdb=" N ARG N 349 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL N 359 " --> pdb=" O VAL N 347 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL N 347 " --> pdb=" O VAL N 359 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR N 439 " --> pdb=" O PHE N 429 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2076 1.32 - 1.44: 4751 1.44 - 1.57: 7353 1.57 - 1.69: 496 1.69 - 1.82: 24 Bond restraints: 14700 Sorted by residual: bond pdb=" N1 DC J 2 " pdb=" C6 DC J 2 " ideal model delta sigma weight residual 1.367 1.390 -0.023 6.00e-03 2.78e+04 1.43e+01 bond pdb=" NE ARG H 31 " pdb=" CZ ARG H 31 " ideal model delta sigma weight residual 1.326 1.366 -0.040 1.10e-02 8.26e+03 1.34e+01 bond pdb=" N1 DC I 23 " pdb=" C6 DC I 23 " ideal model delta sigma weight residual 1.367 1.389 -0.022 6.00e-03 2.78e+04 1.33e+01 bond pdb=" N1 DC I 23 " pdb=" C2 DC I 23 " ideal model delta sigma weight residual 1.397 1.426 -0.029 1.00e-02 1.00e+04 8.21e+00 bond pdb=" CA PRO M 294 " pdb=" C PRO M 294 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.20e+00 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 18515 1.57 - 3.15: 2088 3.15 - 4.72: 356 4.72 - 6.30: 56 6.30 - 7.87: 31 Bond angle restraints: 21046 Sorted by residual: angle pdb=" C LEU D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 angle pdb=" O4' DC J 15 " pdb=" C4' DC J 15 " pdb=" C3' DC J 15 " ideal model delta sigma weight residual 106.00 101.56 4.44 6.00e-01 2.78e+00 5.47e+01 angle pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta sigma weight residual 119.56 126.95 -7.39 1.02e+00 9.61e-01 5.25e+01 angle pdb=" C ASP M 203 " pdb=" N PRO M 204 " pdb=" CA PRO M 204 " ideal model delta sigma weight residual 119.87 127.29 -7.42 1.04e+00 9.25e-01 5.08e+01 angle pdb=" C VAL N 331 " pdb=" N PRO N 332 " pdb=" CA PRO N 332 " ideal model delta sigma weight residual 120.03 127.07 -7.04 9.90e-01 1.02e+00 5.06e+01 ... (remaining 21041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 7173 35.90 - 71.80: 998 71.80 - 107.70: 13 107.70 - 143.60: 0 143.60 - 179.49: 2 Dihedral angle restraints: 8186 sinusoidal: 4293 harmonic: 3893 Sorted by residual: dihedral pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sinusoidal sigma weight residual 220.00 40.51 179.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 133 " pdb=" C3' DG I 133 " pdb=" O3' DG I 133 " pdb=" P DT I 134 " ideal model delta sinusoidal sigma weight residual 220.00 58.70 161.30 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA LEU H 102 " pdb=" C LEU H 102 " pdb=" N PRO H 103 " pdb=" CA PRO H 103 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1585 0.052 - 0.103: 670 0.103 - 0.155: 216 0.155 - 0.206: 17 0.206 - 0.258: 6 Chirality restraints: 2494 Sorted by residual: chirality pdb=" CG LEU F 22 " pdb=" CB LEU F 22 " pdb=" CD1 LEU F 22 " pdb=" CD2 LEU F 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" P DC I 23 " pdb=" OP1 DC I 23 " pdb=" OP2 DC I 23 " pdb=" O5' DC I 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.57 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2491 not shown) Planarity restraints: 1881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 34 " 0.106 2.00e-02 2.50e+03 4.63e-02 6.43e+01 pdb=" N9 DG I 34 " -0.006 2.00e-02 2.50e+03 pdb=" C8 DG I 34 " -0.031 2.00e-02 2.50e+03 pdb=" N7 DG I 34 " -0.045 2.00e-02 2.50e+03 pdb=" C5 DG I 34 " -0.042 2.00e-02 2.50e+03 pdb=" C6 DG I 34 " 0.011 2.00e-02 2.50e+03 pdb=" O6 DG I 34 " 0.079 2.00e-02 2.50e+03 pdb=" N1 DG I 34 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DG I 34 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG I 34 " -0.020 2.00e-02 2.50e+03 pdb=" N3 DG I 34 " -0.027 2.00e-02 2.50e+03 pdb=" C4 DG I 34 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " 0.093 2.00e-02 2.50e+03 4.22e-02 4.89e+01 pdb=" N9 DA I 120 " -0.005 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " -0.019 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " -0.035 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " -0.038 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " -0.032 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 111 " 0.090 2.00e-02 2.50e+03 4.53e-02 4.61e+01 pdb=" N1 DC I 111 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC I 111 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 111 " -0.046 2.00e-02 2.50e+03 pdb=" N3 DC I 111 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 111 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC I 111 " 0.063 2.00e-02 2.50e+03 pdb=" C5 DC I 111 " -0.046 2.00e-02 2.50e+03 pdb=" C6 DC I 111 " -0.043 2.00e-02 2.50e+03 ... (remaining 1878 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3091 2.79 - 3.32: 12704 3.32 - 3.85: 26282 3.85 - 4.37: 30601 4.37 - 4.90: 43872 Nonbonded interactions: 116550 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.263 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.418 3.120 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.500 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O SER H 87 " model vdw 2.516 3.040 nonbonded pdb=" N GLN F 27 " pdb=" OE1 GLN F 27 " model vdw 2.519 3.120 ... (remaining 116545 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 124) } 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=0.00 max=1.00 mean=0.86 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: 4.080 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.008 0.051 14700 Z= 0.539 Angle : 1.104 7.874 21046 Z= 0.829 Chirality : 0.060 0.258 2494 Planarity : 0.008 0.053 1881 Dihedral : 24.393 179.494 5650 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 are not related in a simple way. whole: 1.80 (0.22), residues: 1311 helix: 1.37 (0.18), residues: 740 sheet: 0.95 (0.43), residues: 135 loop : 1.25 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 78 TYR 0.030 0.004 TYR C 57 PHE 0.009 0.001 PHE D 70 TRP 0.000 0.000 TRP M 284 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.54 (14700) covalent geometry : angle 1.10405 / 0.83 (21046) hydrogen bonds : bond 0.15710 / 10.61 ( 976) hydrogen bonds : angle 5.70368 / 4.04 ( 2581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 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: E 84 PHE cc_start: 0.8213 (m-80) cc_final: 0.7984 (m-10) REVERT: E 99 TYR cc_start: 0.8842 (t80) cc_final: 0.8498 (t80) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1259 time to fit residues: 58.0662 Evaluate side-chains 216 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 113 HIS H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.079999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.057687 restraints weight = 124980.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.058912 restraints weight = 58059.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.059815 restraints weight = 35831.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.060057 restraints weight = 26588.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.060495 restraints weight = 22413.081| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14700 Z= 0.215 Angle : 0.781 10.275 21046 Z= 0.449 Chirality : 0.048 0.280 2494 Planarity : 0.005 0.046 1881 Dihedral : 27.749 175.583 4122 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.23 % Allowed : 18.00 % Favored : 77.78 % 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 are not related in a simple way. whole: 2.03 (0.22), residues: 1311 helix: 1.74 (0.18), residues: 749 sheet: 0.68 (0.42), residues: 131 loop : 1.08 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 42 TYR 0.023 0.003 TYR B 88 PHE 0.030 0.002 PHE F 61 TRP 0.000 0.000 TRP M 284 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (14700) covalent geometry : angle 0.78077 / 0.45 (21046) hydrogen bonds : bond 0.06210 / 4.21 ( 976) hydrogen bonds : angle 4.32037 / 3.05 ( 2581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.380 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: D 99 ARG cc_start: 0.9425 (mtp85) cc_final: 0.9064 (mtp85) REVERT: E 104 PHE cc_start: 0.9569 (m-80) cc_final: 0.9353 (m-80) REVERT: E 126 LEU cc_start: 0.9539 (tt) cc_final: 0.9106 (tt) outliers start: 27 outliers final: 17 residues processed: 266 average time/residue: 0.1133 time to fit residues: 43.8503 Evaluate side-chains 225 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 109 optimal weight: 40.0000 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.078712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.056334 restraints weight = 126254.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.057535 restraints weight = 59281.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.058401 restraints weight = 36795.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.058683 restraints weight = 27593.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.059057 restraints weight = 23320.322| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14700 Z= 0.212 Angle : 0.739 9.775 21046 Z= 0.428 Chirality : 0.045 0.238 2494 Planarity : 0.005 0.053 1881 Dihedral : 27.962 176.841 4122 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.85 % Allowed : 18.00 % Favored : 77.15 % 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 are not related in a simple way. whole: 1.73 (0.23), residues: 1311 helix: 1.47 (0.18), residues: 758 sheet: 0.57 (0.43), residues: 139 loop : 0.99 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 95 TYR 0.039 0.002 TYR B 98 PHE 0.017 0.002 PHE F 61 TRP 0.000 0.000 TRP M 284 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 (14700) covalent geometry : angle 0.73919 / 0.43 (21046) hydrogen bonds : bond 0.06214 / 4.20 ( 976) hydrogen bonds : angle 4.13831 / 2.91 ( 2581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.357 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: D 99 ARG cc_start: 0.9342 (mtp85) cc_final: 0.9037 (mtp85) outliers start: 31 outliers final: 21 residues processed: 240 average time/residue: 0.0967 time to fit residues: 34.8010 Evaluate side-chains 221 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 55 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 105 optimal weight: 50.0000 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 147 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** 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 = 0.4186 r_free = 0.4186 target = 0.077470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.055027 restraints weight = 127422.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.056220 restraints weight = 58875.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.057086 restraints weight = 36551.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.057293 restraints weight = 26989.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.057785 restraints weight = 22886.021| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 14700 Z= 0.241 Angle : 0.753 10.153 21046 Z= 0.431 Chirality : 0.045 0.215 2494 Planarity : 0.005 0.055 1881 Dihedral : 28.319 174.559 4122 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.85 % Allowed : 21.13 % Favored : 74.02 % 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 are not related in a simple way. whole: 1.51 (0.23), residues: 1311 helix: 1.37 (0.18), residues: 757 sheet: 0.37 (0.43), residues: 139 loop : 0.77 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 79 TYR 0.024 0.002 TYR G 57 PHE 0.027 0.002 PHE E 104 TRP 0.000 0.000 TRP M 284 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.24 (14700) covalent geometry : angle 0.75311 / 0.43 (21046) hydrogen bonds : bond 0.06478 / 4.39 ( 976) hydrogen bonds : angle 4.21807 / 3.00 ( 2581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 0.437 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 outliers start: 31 outliers final: 20 residues processed: 228 average time/residue: 0.0998 time to fit residues: 34.8844 Evaluate side-chains 211 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 123 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.077058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.054583 restraints weight = 127759.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.055752 restraints weight = 59779.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.056551 restraints weight = 36963.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.056836 restraints weight = 27577.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.057417 restraints weight = 23365.484| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14700 Z= 0.221 Angle : 0.737 10.689 21046 Z= 0.421 Chirality : 0.044 0.207 2494 Planarity : 0.005 0.056 1881 Dihedral : 28.540 174.640 4122 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.32 % Allowed : 22.22 % Favored : 72.46 % 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 are not related in a simple way. whole: 1.46 (0.23), residues: 1311 helix: 1.39 (0.19), residues: 757 sheet: 0.17 (0.43), residues: 141 loop : 0.70 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 95 TYR 0.043 0.003 TYR B 98 PHE 0.014 0.002 PHE H 65 TRP 0.000 0.000 TRP M 284 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 (14700) covalent geometry : angle 0.73688 / 0.42 (21046) hydrogen bonds : bond 0.06068 / 4.11 ( 976) hydrogen bonds : angle 4.14624 / 2.92 ( 2581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 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 outliers start: 34 outliers final: 22 residues processed: 224 average time/residue: 0.0854 time to fit residues: 29.6769 Evaluate side-chains 212 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 133 optimal weight: 50.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** 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 = 0.4169 r_free = 0.4169 target = 0.076600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.054172 restraints weight = 127580.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.055117 restraints weight = 59872.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.055812 restraints weight = 37483.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.056609 restraints weight = 27424.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.056762 restraints weight = 23279.683| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 14700 Z= 0.224 Angle : 0.741 9.147 21046 Z= 0.421 Chirality : 0.044 0.256 2494 Planarity : 0.005 0.058 1881 Dihedral : 28.643 174.093 4122 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.23 % Allowed : 24.88 % Favored : 70.89 % 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 are not related in a simple way. whole: 1.40 (0.23), residues: 1311 helix: 1.37 (0.19), residues: 759 sheet: 0.31 (0.43), residues: 140 loop : 0.54 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.032 0.003 TYR B 88 PHE 0.015 0.002 PHE H 70 TRP 0.000 0.000 TRP M 284 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 (14700) covalent geometry : angle 0.74093 / 0.42 (21046) hydrogen bonds : bond 0.06300 / 4.28 ( 976) hydrogen bonds : angle 4.20444 / 2.98 ( 2581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.413 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: D 99 ARG cc_start: 0.9481 (mtp85) cc_final: 0.8951 (mtp85) outliers start: 27 outliers final: 22 residues processed: 217 average time/residue: 0.0982 time to fit residues: 32.8796 Evaluate side-chains 211 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 143 optimal weight: 50.0000 chunk 88 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** 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 = 0.4173 r_free = 0.4173 target = 0.076775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.054347 restraints weight = 127230.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.055348 restraints weight = 60013.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.056235 restraints weight = 37565.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.056472 restraints weight = 27802.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.056866 restraints weight = 23454.748| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14700 Z= 0.198 Angle : 0.735 11.014 21046 Z= 0.418 Chirality : 0.044 0.274 2494 Planarity : 0.005 0.059 1881 Dihedral : 28.661 174.106 4122 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.01 % Allowed : 25.67 % Favored : 69.33 % 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 are not related in a simple way. whole: 1.33 (0.23), residues: 1311 helix: 1.30 (0.19), residues: 759 sheet: 0.36 (0.46), residues: 131 loop : 0.50 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.030 0.002 TYR G 57 PHE 0.016 0.002 PHE E 104 TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (14700) covalent geometry : angle 0.73455 / 0.42 (21046) hydrogen bonds : bond 0.05755 / 3.90 ( 976) hydrogen bonds : angle 4.15232 / 2.93 ( 2581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.424 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: D 99 ARG cc_start: 0.9482 (mtp85) cc_final: 0.8981 (mtp85) outliers start: 32 outliers final: 21 residues processed: 214 average time/residue: 0.0881 time to fit residues: 29.4439 Evaluate side-chains 209 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 40.0000 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.078128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.055602 restraints weight = 124462.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.056689 restraints weight = 58052.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.057504 restraints weight = 35748.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.057775 restraints weight = 26383.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.058375 restraints weight = 22532.249| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14700 Z= 0.156 Angle : 0.729 13.027 21046 Z= 0.410 Chirality : 0.045 0.257 2494 Planarity : 0.004 0.059 1881 Dihedral : 28.471 174.330 4122 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.50 % Allowed : 27.86 % Favored : 69.64 % 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 are not related in a simple way. whole: 1.45 (0.23), residues: 1311 helix: 1.39 (0.19), residues: 760 sheet: 0.51 (0.44), residues: 140 loop : 0.51 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.025 0.002 TYR G 57 PHE 0.015 0.001 PHE A 67 TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (14700) covalent geometry : angle 0.72926 / 0.41 (21046) hydrogen bonds : bond 0.04410 / 3.03 ( 976) hydrogen bonds : angle 3.93980 / 2.78 ( 2581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.445 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: D 99 ARG cc_start: 0.9412 (mtp85) cc_final: 0.8930 (mtp85) outliers start: 16 outliers final: 11 residues processed: 229 average time/residue: 0.0945 time to fit residues: 33.2082 Evaluate side-chains 210 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 49 optimal weight: 0.9980 chunk 126 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 96 optimal weight: 40.0000 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** 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 = 0.4190 r_free = 0.4190 target = 0.077529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.055073 restraints weight = 126931.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.056141 restraints weight = 59276.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.057079 restraints weight = 36800.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.057332 restraints weight = 27279.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.057668 restraints weight = 23127.077| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14700 Z= 0.174 Angle : 0.738 12.547 21046 Z= 0.416 Chirality : 0.044 0.258 2494 Planarity : 0.004 0.057 1881 Dihedral : 28.419 173.994 4122 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.50 % Allowed : 28.48 % Favored : 69.01 % 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 are not related in a simple way. whole: 1.34 (0.23), residues: 1311 helix: 1.24 (0.19), residues: 763 sheet: 0.61 (0.44), residues: 140 loop : 0.56 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.032 0.002 TYR B 98 PHE 0.016 0.002 PHE A 104 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (14700) covalent geometry : angle 0.73831 / 0.42 (21046) hydrogen bonds : bond 0.05091 / 3.45 ( 976) hydrogen bonds : angle 4.00093 / 2.83 ( 2581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.423 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 outliers start: 16 outliers final: 14 residues processed: 207 average time/residue: 0.0990 time to fit residues: 31.4406 Evaluate side-chains 206 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** 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 = 0.4193 r_free = 0.4193 target = 0.077643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.055166 restraints weight = 125778.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.056327 restraints weight = 58421.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.057181 restraints weight = 36064.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.057645 restraints weight = 26889.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.057779 restraints weight = 22493.568| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14700 Z= 0.171 Angle : 0.743 11.557 21046 Z= 0.421 Chirality : 0.045 0.335 2494 Planarity : 0.004 0.058 1881 Dihedral : 28.414 174.745 4122 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.50 % Allowed : 29.42 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1311 helix: 1.28 (0.19), residues: 763 sheet: 0.43 (0.44), residues: 141 loop : 0.63 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.026 0.002 TYR B 98 PHE 0.029 0.001 PHE E 104 TRP 0.000 0.000 TRP M 284 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14700) covalent geometry : angle 0.74272 / 0.42 (21046) hydrogen bonds : bond 0.04822 / 3.26 ( 976) hydrogen bonds : angle 3.97946 / 2.82 ( 2581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.303 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 outliers start: 16 outliers final: 12 residues processed: 216 average time/residue: 0.0868 time to fit residues: 29.2689 Evaluate side-chains 207 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 84 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 105 optimal weight: 50.0000 chunk 144 optimal weight: 50.0000 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** 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 = 0.4189 r_free = 0.4189 target = 0.077446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.055107 restraints weight = 126302.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.056237 restraints weight = 59152.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.056694 restraints weight = 37043.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.057324 restraints weight = 28325.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.057705 restraints weight = 23793.671| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14700 Z= 0.181 Angle : 0.758 13.421 21046 Z= 0.429 Chirality : 0.046 0.633 2494 Planarity : 0.004 0.059 1881 Dihedral : 28.425 174.817 4122 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.19 % Allowed : 30.67 % Favored : 67.14 % 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 are not related in a simple way. whole: 1.42 (0.23), residues: 1311 helix: 1.31 (0.19), residues: 763 sheet: 0.44 (0.44), residues: 141 loop : 0.67 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.036 0.003 TYR B 88 PHE 0.033 0.002 PHE A 104 TRP 0.000 0.000 TRP M 284 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (14700) covalent geometry : angle 0.75838 / 0.43 (21046) hydrogen bonds : bond 0.05093 / 3.43 ( 976) hydrogen bonds : angle 4.03581 / 2.85 ( 2581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4192.12 seconds wall clock time: 71 minutes 44.38 seconds (4304.38 seconds total)