Starting phenix.real_space_refine on Sat Aug 23 18:09:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osk_17157/08_2025/8osk_17157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osk_17157/08_2025/8osk_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_17157/08_2025/8osk_17157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osk_17157/08_2025/8osk_17157.map" model { file = "/net/cci-nas-00/data/ceres_data/8osk_17157/08_2025/8osk_17157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osk_17157/08_2025/8osk_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-2.0-5787/lib/python3.9/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: 2.63, per 1000 atoms: 0.19 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 464.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.19 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: 3.01 Time building geometry restraints manager: 1.45 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=" 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=" 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 bond pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.41e+00 bond pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.40e+00 bond pdb=" NE ARG F 40 " pdb=" CZ ARG F 40 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.35e+00 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 18377 1.57 - 3.15: 2234 3.15 - 4.72: 348 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=" 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 angle pdb=" C LEU H 102 " pdb=" N PRO H 103 " pdb=" CA PRO H 103 " ideal model delta sigma weight residual 119.78 127.01 -7.23 1.03e+00 9.43e-01 4.93e+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: 1673 0.052 - 0.103: 583 0.103 - 0.155: 215 0.155 - 0.206: 19 0.206 - 0.258: 4 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 2.35 -2.57 -0.22 2.00e-01 2.50e+01 1.25e+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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.850 Find NCS groups from input model: 0.140 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: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.009 0.051 14700 Z= 0.475 Angle : 1.122 7.874 21046 Z= 0.762 Chirality : 0.058 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 aren 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 covalent geometry : bond 0.00861 (14700) covalent geometry : angle 1.12219 (21046) hydrogen bonds : bond 0.15710 ( 976) hydrogen bonds : angle 5.70368 ( 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 : 0.335 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: 0.1133 time to fit residues: 51.7781 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 : 0.321 ------------------------------------------------------------------------------- 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: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 84 ASN E 113 HIS H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.079637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.057246 restraints weight = 125202.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.058414 restraints weight = 57869.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.059379 restraints weight = 36092.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.059641 restraints weight = 26683.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.059948 restraints weight = 22253.163| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14700 Z= 0.192 Angle : 0.668 12.091 21046 Z= 0.384 Chirality : 0.040 0.135 2494 Planarity : 0.004 0.033 1881 Dihedral : 27.595 177.805 4122 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.60 % Allowed : 16.90 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.37 (0.23), residues: 1311 helix: 2.02 (0.18), residues: 760 sheet: 0.95 (0.45), residues: 129 loop : 1.14 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.022 0.002 TYR B 88 PHE 0.014 0.002 PHE F 61 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (14700) covalent geometry : angle 0.66767 (21046) hydrogen bonds : bond 0.05123 ( 976) hydrogen bonds : angle 3.85376 ( 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 280 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.293 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: A 104 PHE cc_start: 0.9138 (m-80) cc_final: 0.8835 (m-80) REVERT: D 99 ARG cc_start: 0.9411 (mtp85) cc_final: 0.9147 (mtp85) outliers start: 23 outliers final: 12 residues processed: 265 average time/residue: 0.1040 time to fit residues: 39.8493 Evaluate side-chains 225 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 110 ASN 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 49 LEU 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 64 GLU Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.074272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.052086 restraints weight = 130383.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.053065 restraints weight = 62499.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.053525 restraints weight = 39911.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.054087 restraints weight = 31177.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.054636 restraints weight = 26125.172| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 14700 Z= 0.391 Angle : 0.759 8.575 21046 Z= 0.440 Chirality : 0.045 0.174 2494 Planarity : 0.005 0.055 1881 Dihedral : 28.922 176.448 4122 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 6.73 % Allowed : 18.00 % Favored : 75.27 % 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: 1.65 (0.23), residues: 1311 helix: 1.40 (0.18), residues: 771 sheet: 0.36 (0.44), residues: 131 loop : 1.03 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.034 0.003 TYR B 98 PHE 0.026 0.002 PHE G 25 TRP 0.000 0.000 TRP M 284 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00844 (14700) covalent geometry : angle 0.75899 (21046) hydrogen bonds : bond 0.08609 ( 976) hydrogen bonds : angle 4.43386 ( 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 253 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.9201 (m-80) cc_final: 0.8864 (m-80) REVERT: F 46 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9236 (pt) outliers start: 43 outliers final: 30 residues processed: 229 average time/residue: 0.0896 time to fit residues: 31.3146 Evaluate side-chains 208 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 85 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 110 ASN 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 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 64 ASN 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 93 GLN 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 G residue 108 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 50.0000 chunk 21 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** 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 = 0.4161 r_free = 0.4161 target = 0.076264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.054041 restraints weight = 126385.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.054983 restraints weight = 59282.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.055396 restraints weight = 36886.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.055965 restraints weight = 28374.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.056499 restraints weight = 23612.939| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14700 Z= 0.207 Angle : 0.654 11.095 21046 Z= 0.376 Chirality : 0.040 0.174 2494 Planarity : 0.004 0.041 1881 Dihedral : 28.657 176.153 4122 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.44 % Allowed : 23.47 % Favored : 73.08 % 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 aren not related in a simple way. whole: 1.88 (0.23), residues: 1311 helix: 1.71 (0.18), residues: 766 sheet: 0.29 (0.43), residues: 139 loop : 0.92 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.019 0.002 TYR B 88 PHE 0.020 0.002 PHE H 65 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (14700) covalent geometry : angle 0.65416 (21046) hydrogen bonds : bond 0.04916 ( 976) hydrogen bonds : angle 3.93429 ( 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 232 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.419 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: A 104 PHE cc_start: 0.9217 (m-80) cc_final: 0.8828 (m-80) REVERT: F 46 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9214 (pt) REVERT: G 82 HIS cc_start: 0.9086 (m170) cc_final: 0.8852 (m90) outliers start: 22 outliers final: 13 residues processed: 218 average time/residue: 0.0824 time to fit residues: 28.0847 Evaluate side-chains 202 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 50.0000 chunk 38 optimal weight: 0.9990 chunk 131 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4160 r_free = 0.4160 target = 0.076145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.053717 restraints weight = 127028.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.054859 restraints weight = 59736.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.055712 restraints weight = 37619.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.055930 restraints weight = 28403.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.056004 restraints weight = 24294.495| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14700 Z= 0.210 Angle : 0.648 9.600 21046 Z= 0.372 Chirality : 0.040 0.164 2494 Planarity : 0.004 0.050 1881 Dihedral : 28.464 176.802 4122 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.60 % Allowed : 24.41 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.23), residues: 1311 helix: 1.77 (0.18), residues: 763 sheet: 0.41 (0.44), residues: 138 loop : 0.83 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.040 0.002 TYR B 98 PHE 0.017 0.002 PHE D 65 TRP 0.000 0.000 TRP M 284 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (14700) covalent geometry : angle 0.64791 (21046) hydrogen bonds : bond 0.05110 ( 976) hydrogen bonds : angle 3.82404 ( 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 224 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.260 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: A 104 PHE cc_start: 0.9217 (m-80) cc_final: 0.8836 (m-80) REVERT: H 95 GLN cc_start: 0.9006 (pp30) cc_final: 0.8754 (pp30) outliers start: 23 outliers final: 12 residues processed: 209 average time/residue: 0.0751 time to fit residues: 24.5058 Evaluate side-chains 192 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain E residue 46 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 93 GLN 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 G residue 83 LEU Chi-restraints excluded: chain H residue 52 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: 6.9990 chunk 91 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 40.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4136 r_free = 0.4136 target = 0.075094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.053010 restraints weight = 127980.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.053884 restraints weight = 61072.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.054370 restraints weight = 38364.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.055158 restraints weight = 29600.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.055322 restraints weight = 24888.013| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14700 Z= 0.261 Angle : 0.677 14.260 21046 Z= 0.388 Chirality : 0.041 0.201 2494 Planarity : 0.004 0.052 1881 Dihedral : 28.737 177.715 4122 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.07 % Allowed : 25.82 % Favored : 70.11 % 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: 1.91 (0.23), residues: 1311 helix: 1.76 (0.18), residues: 751 sheet: 0.62 (0.44), residues: 139 loop : 0.80 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 92 TYR 0.033 0.002 TYR B 98 PHE 0.012 0.002 PHE A 67 TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00566 (14700) covalent geometry : angle 0.67692 (21046) hydrogen bonds : bond 0.05894 ( 976) hydrogen bonds : angle 3.97441 ( 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 214 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 196 average time/residue: 0.0956 time to fit residues: 29.0662 Evaluate side-chains 196 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER 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 93 GLN 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 G residue 83 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 96 optimal weight: 50.0000 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 143 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4128 r_free = 0.4128 target = 0.074963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.052724 restraints weight = 127324.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.053639 restraints weight = 62131.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.054406 restraints weight = 38829.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.054650 restraints weight = 29278.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.055249 restraints weight = 25427.263| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14700 Z= 0.256 Angle : 0.682 10.139 21046 Z= 0.390 Chirality : 0.041 0.193 2494 Planarity : 0.005 0.054 1881 Dihedral : 28.764 177.841 4122 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.44 % Allowed : 28.33 % Favored : 68.23 % 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: 1.90 (0.23), residues: 1311 helix: 1.75 (0.18), residues: 747 sheet: 0.54 (0.45), residues: 139 loop : 0.83 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 33 TYR 0.026 0.002 TYR B 98 PHE 0.011 0.001 PHE A 67 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00555 (14700) covalent geometry : angle 0.68224 (21046) hydrogen bonds : bond 0.05732 ( 976) hydrogen bonds : angle 3.97263 ( 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 205 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 193 average time/residue: 0.0961 time to fit residues: 28.7586 Evaluate side-chains 191 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain E residue 46 VAL 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 F residue 87 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4162 r_free = 0.4162 target = 0.076496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.054218 restraints weight = 124301.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.055203 restraints weight = 59777.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.056077 restraints weight = 37683.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.056330 restraints weight = 28486.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.056694 restraints weight = 24237.033| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14700 Z= 0.176 Angle : 0.663 14.795 21046 Z= 0.376 Chirality : 0.039 0.177 2494 Planarity : 0.004 0.055 1881 Dihedral : 28.480 178.163 4122 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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 aren not related in a simple way. whole: 1.97 (0.23), residues: 1311 helix: 1.89 (0.19), residues: 751 sheet: 0.36 (0.44), residues: 140 loop : 0.74 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.027 0.002 TYR B 98 PHE 0.010 0.001 PHE A 67 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (14700) covalent geometry : angle 0.66319 (21046) hydrogen bonds : bond 0.04275 ( 976) hydrogen bonds : angle 3.79374 ( 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 210 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.327 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: G 82 HIS cc_start: 0.9107 (m90) cc_final: 0.8738 (m90) outliers start: 16 outliers final: 14 residues processed: 201 average time/residue: 0.0969 time to fit residues: 30.2483 Evaluate side-chains 196 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain E residue 46 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 87 VAL Chi-restraints excluded: chain F residue 93 GLN 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 G residue 83 LEU 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: 6.9990 chunk 42 optimal weight: 0.7980 chunk 110 optimal weight: 30.0000 chunk 96 optimal weight: 50.0000 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4186 r_free = 0.4186 target = 0.077449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.055520 restraints weight = 124419.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.055980 restraints weight = 62896.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.056565 restraints weight = 37724.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.057075 restraints weight = 28353.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.057640 restraints weight = 23329.831| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14700 Z= 0.160 Angle : 0.674 15.178 21046 Z= 0.378 Chirality : 0.039 0.226 2494 Planarity : 0.004 0.056 1881 Dihedral : 28.187 178.631 4122 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.88 % Allowed : 30.52 % Favored : 67.61 % 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: 1.91 (0.24), residues: 1311 helix: 1.80 (0.19), residues: 757 sheet: 0.43 (0.44), residues: 140 loop : 0.76 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.030 0.002 TYR B 98 PHE 0.010 0.001 PHE E 104 TRP 0.000 0.000 TRP M 284 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00350 (14700) covalent geometry : angle 0.67391 (21046) hydrogen bonds : bond 0.03860 ( 976) hydrogen bonds : angle 3.69624 ( 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 215 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.375 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 84 ASN cc_start: 0.8653 (t0) cc_final: 0.8208 (t0) REVERT: E 104 PHE cc_start: 0.9551 (m-10) cc_final: 0.9350 (m-80) REVERT: G 82 HIS cc_start: 0.9160 (m90) cc_final: 0.8731 (m90) outliers start: 12 outliers final: 11 residues processed: 208 average time/residue: 0.0899 time to fit residues: 29.2814 Evaluate side-chains 200 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 GLN 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 G residue 83 LEU Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 144 optimal weight: 50.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4160 r_free = 0.4160 target = 0.076209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.054382 restraints weight = 125460.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.054793 restraints weight = 64352.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.055407 restraints weight = 39713.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.055877 restraints weight = 30030.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.055994 restraints weight = 24555.426| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14700 Z= 0.209 Angle : 0.700 14.718 21046 Z= 0.394 Chirality : 0.041 0.219 2494 Planarity : 0.004 0.058 1881 Dihedral : 28.351 179.367 4122 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.88 % Allowed : 31.30 % Favored : 66.82 % 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: 1.74 (0.24), residues: 1311 helix: 1.64 (0.19), residues: 767 sheet: 0.40 (0.45), residues: 134 loop : 0.68 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.029 0.002 TYR B 98 PHE 0.018 0.002 PHE H 65 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00460 (14700) covalent geometry : angle 0.69973 (21046) hydrogen bonds : bond 0.04919 ( 976) hydrogen bonds : angle 3.82377 ( 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 200 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.393 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: D 84 ASN cc_start: 0.8686 (t0) cc_final: 0.8220 (t0) REVERT: G 82 HIS cc_start: 0.9062 (m90) cc_final: 0.8712 (m90) outliers start: 12 outliers final: 11 residues processed: 194 average time/residue: 0.0866 time to fit residues: 26.1301 Evaluate side-chains 190 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 105 optimal weight: 50.0000 chunk 144 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4147 r_free = 0.4147 target = 0.075582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.053294 restraints weight = 126134.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.054238 restraints weight = 60833.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.055154 restraints weight = 39440.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.055422 restraints weight = 29638.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.055919 restraints weight = 25278.316| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14700 Z= 0.230 Angle : 0.721 14.079 21046 Z= 0.405 Chirality : 0.042 0.253 2494 Planarity : 0.004 0.058 1881 Dihedral : 28.526 178.336 4122 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.72 % Allowed : 31.61 % Favored : 66.67 % 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: 1.65 (0.24), residues: 1311 helix: 1.58 (0.19), residues: 769 sheet: 0.37 (0.45), residues: 134 loop : 0.59 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.027 0.002 TYR B 98 PHE 0.036 0.002 PHE B 61 TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00505 (14700) covalent geometry : angle 0.72092 (21046) hydrogen bonds : bond 0.05273 ( 976) hydrogen bonds : angle 3.96787 ( 2581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.96 seconds wall clock time: 68 minutes 56.55 seconds (4136.55 seconds total)