Starting phenix.real_space_refine on Fri May 16 01:21:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osk_17157/05_2025/8osk_17157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osk_17157/05_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_17157/05_2025/8osk_17157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osk_17157/05_2025/8osk_17157.map" model { file = "/net/cci-nas-00/data/ceres_data/8osk_17157/05_2025/8osk_17157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osk_17157/05_2025/8osk_17157.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 12, 'HIS:plan': 13, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 18, 'GLU:plan': 28, 'ARG:plan': 15} 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: {'GLN:plan1': 11, 'HIS:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 14, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 517 Time building chain proxies: 8.48, per 1000 atoms: 0.61 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: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 6.61 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: 6.73 Time building geometry restraints manager: 4.16 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: 2.720 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: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 39.710 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (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 TRP 0.000 0.000 TRP M 284 HIS 0.003 0.001 HIS H 49 PHE 0.009 0.001 PHE D 70 TYR 0.030 0.004 TYR C 57 ARG 0.007 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.15710 ( 976) hydrogen bonds : angle 5.70368 ( 2581) covalent geometry : bond 0.00861 (14700) covalent geometry : angle 1.12219 (21046) *********************** 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 : 1.207 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: 0.2831 time to fit residues: 128.2357 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 40.0000 chunk 117 optimal weight: 50.0000 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4191 r_free = 0.4191 target = 0.077787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.055441 restraints weight = 126374.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.056672 restraints weight = 59317.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.057543 restraints weight = 36807.853| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14700 Z= 0.261 Angle : 0.689 12.111 21046 Z= 0.400 Chirality : 0.041 0.138 2494 Planarity : 0.005 0.035 1881 Dihedral : 27.887 179.883 4122 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.85 % Allowed : 17.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.23), residues: 1311 helix: 1.84 (0.18), residues: 764 sheet: 0.85 (0.44), residues: 129 loop : 1.15 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.002 HIS B 75 PHE 0.017 0.002 PHE B 100 TYR 0.024 0.002 TYR B 88 ARG 0.008 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06028 ( 976) hydrogen bonds : angle 4.04182 ( 2581) covalent geometry : bond 0.00556 (14700) covalent geometry : angle 0.68884 (21046) *********************** 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 275 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 1.125 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: 0.9209 (m-80) cc_final: 0.8888 (m-80) REVERT: D 95 GLN cc_start: 0.9311 (tt0) cc_final: 0.9020 (tm-30) REVERT: D 99 ARG cc_start: 0.9425 (mtp85) cc_final: 0.8859 (mtp85) REVERT: E 104 PHE cc_start: 0.9570 (m-80) cc_final: 0.9318 (m-80) outliers start: 31 outliers final: 19 residues processed: 254 average time/residue: 0.2454 time to fit residues: 90.9443 Evaluate side-chains 227 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN 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 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 H residue 39 ILE Chi-restraints excluded: chain H residue 44 VAL 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 8 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 44 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.077996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.055663 restraints weight = 125844.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.056718 restraints weight = 58327.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.057578 restraints weight = 35749.692| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3777 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= 0.193 Angle : 0.647 9.838 21046 Z= 0.372 Chirality : 0.039 0.169 2494 Planarity : 0.004 0.061 1881 Dihedral : 28.047 178.523 4122 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.60 % Allowed : 18.00 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.23), residues: 1311 helix: 1.89 (0.18), residues: 752 sheet: 0.79 (0.45), residues: 129 loop : 1.01 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE D 65 TYR 0.034 0.002 TYR B 98 ARG 0.006 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 976) hydrogen bonds : angle 3.79524 ( 2581) covalent geometry : bond 0.00412 (14700) covalent geometry : angle 0.64664 (21046) *********************** 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: 23 poor density : 234 time to evaluate : 1.167 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: A 104 PHE cc_start: 0.9238 (m-80) cc_final: 0.8898 (m-80) REVERT: D 95 GLN cc_start: 0.9326 (tt0) cc_final: 0.8995 (tm-30) REVERT: D 99 ARG cc_start: 0.9381 (mtp85) cc_final: 0.8728 (mtp85) outliers start: 23 outliers final: 10 residues processed: 243 average time/residue: 0.2458 time to fit residues: 87.6300 Evaluate side-chains 207 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 87 ILE Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 142 optimal weight: 50.0000 chunk 50 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.078660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.056351 restraints weight = 124344.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.057381 restraints weight = 57215.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.058387 restraints weight = 36095.129| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14700 Z= 0.160 Angle : 0.632 13.401 21046 Z= 0.359 Chirality : 0.038 0.172 2494 Planarity : 0.004 0.066 1881 Dihedral : 27.848 178.398 4122 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.44 % Allowed : 21.44 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.23), residues: 1311 helix: 1.92 (0.18), residues: 762 sheet: 0.79 (0.45), residues: 129 loop : 0.83 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.005 0.001 HIS F 75 PHE 0.014 0.001 PHE B 100 TYR 0.020 0.002 TYR B 98 ARG 0.005 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 976) hydrogen bonds : angle 3.60201 ( 2581) covalent geometry : bond 0.00346 (14700) covalent geometry : angle 0.63187 (21046) *********************** 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 250 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.9200 (m-80) cc_final: 0.8826 (m-80) REVERT: D 95 GLN cc_start: 0.9326 (tt0) cc_final: 0.8946 (tm-30) REVERT: D 99 ARG cc_start: 0.9355 (mtp85) cc_final: 0.8673 (mtp85) outliers start: 22 outliers final: 16 residues processed: 235 average time/residue: 0.2235 time to fit residues: 79.4418 Evaluate side-chains 215 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain C residue 110 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 100 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 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 50.0000 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 133 optimal weight: 50.0000 chunk 70 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.077387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.054996 restraints weight = 126601.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.056168 restraints weight = 58991.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.056613 restraints weight = 36336.512| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14700 Z= 0.193 Angle : 0.637 11.076 21046 Z= 0.365 Chirality : 0.039 0.173 2494 Planarity : 0.004 0.062 1881 Dihedral : 27.964 178.619 4122 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.97 % Allowed : 24.26 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.23), residues: 1311 helix: 1.84 (0.18), residues: 763 sheet: 0.64 (0.45), residues: 129 loop : 0.92 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE B 61 TYR 0.029 0.002 TYR E 54 ARG 0.003 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 976) hydrogen bonds : angle 3.67891 ( 2581) covalent geometry : bond 0.00424 (14700) covalent geometry : angle 0.63736 (21046) *********************** 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 231 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.081 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: A 104 PHE cc_start: 0.9247 (m-80) cc_final: 0.8832 (m-80) REVERT: G 82 HIS cc_start: 0.9138 (m170) cc_final: 0.8861 (m90) REVERT: H 95 GLN cc_start: 0.8988 (pp30) cc_final: 0.8679 (pp30) outliers start: 19 outliers final: 10 residues processed: 218 average time/residue: 0.2331 time to fit residues: 77.2406 Evaluate side-chains 200 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 97 GLU 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 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 LEU 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 117 optimal weight: 50.0000 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 108 optimal weight: 50.0000 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.075270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.052934 restraints weight = 128683.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.053995 restraints weight = 61336.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.054189 restraints weight = 38672.913| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14700 Z= 0.274 Angle : 0.690 11.787 21046 Z= 0.395 Chirality : 0.042 0.369 2494 Planarity : 0.005 0.067 1881 Dihedral : 28.573 178.577 4122 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.76 % Allowed : 26.45 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1311 helix: 1.60 (0.18), residues: 769 sheet: 0.53 (0.44), residues: 140 loop : 0.97 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 PHE 0.014 0.002 PHE B 61 TYR 0.038 0.003 TYR B 88 ARG 0.004 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.06376 ( 976) hydrogen bonds : angle 4.02902 ( 2581) covalent geometry : bond 0.00595 (14700) covalent geometry : angle 0.68966 (21046) *********************** 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 216 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.200 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: 0.9227 (m-80) cc_final: 0.8835 (m-80) REVERT: H 95 GLN cc_start: 0.9032 (pp30) cc_final: 0.8688 (pp30) outliers start: 24 outliers final: 17 residues processed: 201 average time/residue: 0.2047 time to fit residues: 63.3816 Evaluate side-chains 197 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 97 GLU 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 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 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 87 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 96 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 143 optimal weight: 40.0000 chunk 140 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.074953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.052672 restraints weight = 128326.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.053719 restraints weight = 60678.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.054553 restraints weight = 38754.315| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14700 Z= 0.276 Angle : 0.691 11.400 21046 Z= 0.397 Chirality : 0.042 0.347 2494 Planarity : 0.005 0.054 1881 Dihedral : 28.761 178.260 4122 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.76 % Allowed : 27.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.23), residues: 1311 helix: 1.46 (0.18), residues: 769 sheet: 0.66 (0.44), residues: 139 loop : 0.86 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 PHE 0.026 0.002 PHE E 104 TYR 0.037 0.002 TYR B 88 ARG 0.003 0.001 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 976) hydrogen bonds : angle 4.08983 ( 2581) covalent geometry : bond 0.00599 (14700) covalent geometry : angle 0.69082 (21046) *********************** 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 210 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 GLN cc_start: 0.8977 (pp30) cc_final: 0.8629 (pp30) outliers start: 24 outliers final: 19 residues processed: 196 average time/residue: 0.2210 time to fit residues: 66.4992 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 : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain D residue 52 THR 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 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 150 optimal weight: 50.0000 chunk 106 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 140 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.076156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.053718 restraints weight = 125857.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.054645 restraints weight = 59096.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.055260 restraints weight = 37529.965| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14700 Z= 0.200 Angle : 0.685 15.553 21046 Z= 0.384 Chirality : 0.041 0.384 2494 Planarity : 0.004 0.047 1881 Dihedral : 28.548 178.499 4122 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.19 % Allowed : 29.42 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.23), residues: 1311 helix: 1.57 (0.18), residues: 769 sheet: 0.44 (0.44), residues: 140 loop : 0.86 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.006 0.001 HIS F 75 PHE 0.026 0.002 PHE E 104 TYR 0.036 0.002 TYR B 88 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 976) hydrogen bonds : angle 3.88644 ( 2581) covalent geometry : bond 0.00438 (14700) covalent geometry : angle 0.68499 (21046) *********************** 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 208 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 1.182 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: A 104 PHE cc_start: 0.9250 (m-80) cc_final: 0.8898 (m-80) REVERT: E 100 LEU cc_start: 0.8919 (tt) cc_final: 0.8677 (tp) outliers start: 14 outliers final: 12 residues processed: 200 average time/residue: 0.2279 time to fit residues: 69.3646 Evaluate side-chains 189 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 96 THR 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 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 108 LEU 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 15 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 134 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 150 optimal weight: 40.0000 overall best weight: 1.2030 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.077513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.055289 restraints weight = 123677.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.056383 restraints weight = 58359.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.057337 restraints weight = 36512.922| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14700 Z= 0.165 Angle : 0.698 15.366 21046 Z= 0.387 Chirality : 0.041 0.326 2494 Planarity : 0.004 0.046 1881 Dihedral : 28.260 178.472 4122 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 30.36 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1311 helix: 1.56 (0.18), residues: 765 sheet: 0.53 (0.44), residues: 140 loop : 0.90 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.006 0.001 HIS F 75 PHE 0.014 0.001 PHE E 104 TYR 0.018 0.002 TYR A 99 ARG 0.005 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 976) hydrogen bonds : angle 3.79140 ( 2581) covalent geometry : bond 0.00364 (14700) covalent geometry : angle 0.69768 (21046) *********************** 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: 15 poor density : 200 time to evaluate : 1.204 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: 15 outliers final: 10 residues processed: 204 average time/residue: 0.2288 time to fit residues: 70.5475 Evaluate side-chains 197 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 96 THR 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 97 LEU 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 53 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 105 optimal weight: 50.0000 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.076250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.054005 restraints weight = 125530.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.055041 restraints weight = 59597.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.055988 restraints weight = 37692.811| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14700 Z= 0.231 Angle : 0.726 15.662 21046 Z= 0.404 Chirality : 0.042 0.305 2494 Planarity : 0.004 0.044 1881 Dihedral : 28.375 179.198 4122 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.50 % Allowed : 30.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1311 helix: 1.43 (0.18), residues: 769 sheet: 0.49 (0.44), residues: 140 loop : 0.85 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.014 0.002 HIS G 31 PHE 0.023 0.002 PHE B 61 TYR 0.017 0.002 TYR A 99 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.05136 ( 976) hydrogen bonds : angle 3.98620 ( 2581) covalent geometry : bond 0.00514 (14700) covalent geometry : angle 0.72568 (21046) ********************** 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 202 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 1.125 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 outliers start: 16 outliers final: 13 residues processed: 191 average time/residue: 0.2204 time to fit residues: 64.6119 Evaluate side-chains 192 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 98 TYR 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 97 LEU 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 151 optimal weight: 50.0000 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 115 optimal weight: 0.0000 chunk 95 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.076565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.054863 restraints weight = 126112.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.055197 restraints weight = 63861.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.055886 restraints weight = 38894.317| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14700 Z= 0.200 Angle : 0.728 15.359 21046 Z= 0.403 Chirality : 0.042 0.304 2494 Planarity : 0.004 0.041 1881 Dihedral : 28.369 178.592 4122 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 30.67 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1311 helix: 1.35 (0.18), residues: 769 sheet: 0.46 (0.45), residues: 134 loop : 0.80 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.013 0.002 HIS G 31 PHE 0.035 0.002 PHE B 61 TYR 0.022 0.002 TYR G 57 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 976) hydrogen bonds : angle 3.98164 ( 2581) covalent geometry : bond 0.00447 (14700) covalent geometry : angle 0.72758 (21046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7723.26 seconds wall clock time: 133 minutes 25.12 seconds (8005.12 seconds total)