Starting phenix.real_space_refine on Sun Nov 17 13:45:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/11_2024/8osk_17157.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/11_2024/8osk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/11_2024/8osk_17157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/11_2024/8osk_17157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/11_2024/8osk_17157.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/11_2024/8osk_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-5513/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: 9.28, per 1000 atoms: 0.66 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 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: 6.71 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: 6.87 Time building geometry restraints manager: 4.03 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: 2.890 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 41.670 Find NCS groups from input model: 0.310 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- 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= 0.531 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 *********************** 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 : 1.217 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: 0.2892 time to fit residues: 130.8731 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 : 1.214 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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= 0.313 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 *********************** 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 : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 ARG cc_start: 0.9489 (mtp85) cc_final: 0.9099 (mtp85) REVERT: E 84 PHE cc_start: 0.8493 (m-80) cc_final: 0.8225 (m-80) outliers start: 31 outliers final: 19 residues processed: 254 average time/residue: 0.2559 time to fit residues: 94.5969 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 : 1.262 ------------------------------------------------------------------------------- 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 78 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 141 optimal weight: 50.0000 chunk 152 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 14700 Z= 0.421 Angle : 0.738 11.482 21046 Z= 0.427 Chirality : 0.044 0.184 2494 Planarity : 0.005 0.062 1881 Dihedral : 28.934 176.287 4122 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.57 % Allowed : 17.84 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.23), residues: 1311 helix: 1.41 (0.18), residues: 755 sheet: 0.28 (0.44), residues: 129 loop : 0.96 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.009 0.002 HIS F 75 PHE 0.021 0.002 PHE G 25 TYR 0.033 0.002 TYR B 98 ARG 0.008 0.001 ARG G 29 *********************** 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 254 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 1.278 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: 42 outliers final: 24 residues processed: 228 average time/residue: 0.2431 time to fit residues: 82.2820 Evaluate side-chains 207 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 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 64 GLU 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 99 TYR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 ILE 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 139 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 50.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** E 108 ASN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14700 Z= 0.232 Angle : 0.656 12.718 21046 Z= 0.374 Chirality : 0.039 0.167 2494 Planarity : 0.004 0.058 1881 Dihedral : 28.562 175.584 4122 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.60 % Allowed : 21.13 % 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 (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: 1.82 (0.23), residues: 1311 helix: 1.72 (0.19), residues: 762 sheet: 0.29 (0.43), residues: 139 loop : 0.77 (0.31), residues: 410 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 0.021 0.002 PHE H 65 TYR 0.022 0.002 TYR H 121 ARG 0.010 0.001 ARG G 17 *********************** 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 241 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.220 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 outliers start: 23 outliers final: 12 residues processed: 227 average time/residue: 0.2264 time to fit residues: 78.3491 Evaluate side-chains 199 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 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 93 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 43 VAL 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 85 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 111 optimal weight: 50.0000 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 14700 Z= 0.405 Angle : 0.724 11.303 21046 Z= 0.417 Chirality : 0.043 0.194 2494 Planarity : 0.005 0.054 1881 Dihedral : 29.012 176.926 4122 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.85 % Allowed : 23.47 % Favored : 71.67 % 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: 1.58 (0.23), residues: 1311 helix: 1.50 (0.19), residues: 762 sheet: 0.38 (0.43), residues: 137 loop : 0.65 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.009 0.002 HIS F 75 PHE 0.016 0.002 PHE E 104 TYR 0.035 0.003 TYR B 98 ARG 0.005 0.001 ARG E 40 *********************** 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 215 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 26 residues processed: 196 average time/residue: 0.2278 time to fit residues: 68.2548 Evaluate side-chains 198 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 87 VAL 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 68 ASP Chi-restraints excluded: chain F residue 87 VAL 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 80 PRO Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 69 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14700 Z= 0.226 Angle : 0.659 10.873 21046 Z= 0.376 Chirality : 0.039 0.203 2494 Planarity : 0.004 0.050 1881 Dihedral : 28.624 176.520 4122 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.35 % Allowed : 27.54 % 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 (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: 1.82 (0.23), residues: 1311 helix: 1.74 (0.19), residues: 763 sheet: 0.29 (0.43), residues: 140 loop : 0.72 (0.32), residues: 408 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 0.027 0.002 PHE E 104 TYR 0.026 0.002 TYR E 54 ARG 0.004 0.000 ARG B 92 *********************** 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 219 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 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: symmetry clash REVERT: E 104 PHE cc_start: 0.9071 (m-80) cc_final: 0.8721 (m-80) outliers start: 15 outliers final: 11 residues processed: 209 average time/residue: 0.2189 time to fit residues: 70.5971 Evaluate side-chains 195 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 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 H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14700 Z= 0.317 Angle : 0.685 9.585 21046 Z= 0.392 Chirality : 0.041 0.188 2494 Planarity : 0.005 0.052 1881 Dihedral : 28.701 178.290 4122 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.76 % Allowed : 28.95 % 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: 1.73 (0.23), residues: 1311 helix: 1.68 (0.19), residues: 763 sheet: 0.19 (0.43), residues: 140 loop : 0.68 (0.32), residues: 408 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 0.012 0.002 PHE E 104 TYR 0.035 0.002 TYR B 88 ARG 0.003 0.000 ARG B 92 *********************** 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 208 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.265 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: 24 outliers final: 16 residues processed: 194 average time/residue: 0.2546 time to fit residues: 76.7526 Evaluate side-chains 190 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 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 54 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 117 optimal weight: 50.0000 chunk 135 optimal weight: 0.0970 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14700 Z= 0.200 Angle : 0.671 12.749 21046 Z= 0.379 Chirality : 0.039 0.188 2494 Planarity : 0.004 0.053 1881 Dihedral : 28.268 177.935 4122 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 1.81 (0.23), residues: 1311 helix: 1.72 (0.19), residues: 763 sheet: 0.38 (0.44), residues: 140 loop : 0.70 (0.32), residues: 408 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 0.012 0.001 PHE A 67 TYR 0.035 0.002 TYR B 88 ARG 0.006 0.000 ARG H 92 *********************** 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 215 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 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 outliers start: 13 outliers final: 8 residues processed: 207 average time/residue: 0.2248 time to fit residues: 71.9090 Evaluate side-chains 191 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 65 LEU 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 H residue 48 VAL Chi-restraints excluded: chain H residue 54 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 50.0000 chunk 130 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 30.0000 chunk 131 optimal weight: 50.0000 chunk 138 optimal weight: 40.0000 chunk 91 optimal weight: 7.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 14700 Z= 0.336 Angle : 0.713 14.141 21046 Z= 0.406 Chirality : 0.042 0.240 2494 Planarity : 0.005 0.047 1881 Dihedral : 28.615 179.630 4122 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.50 % Allowed : 30.67 % 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 (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: 1.55 (0.23), residues: 1311 helix: 1.49 (0.18), residues: 763 sheet: 0.18 (0.45), residues: 134 loop : 0.67 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.002 HIS F 75 PHE 0.012 0.002 PHE A 67 TYR 0.038 0.002 TYR B 88 ARG 0.004 0.000 ARG A 83 *********************** 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 201 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 193 average time/residue: 0.2194 time to fit residues: 64.9441 Evaluate side-chains 186 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 65 LEU 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 H residue 48 VAL Chi-restraints excluded: chain H residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 50.0000 chunk 154 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 14700 Z= 0.278 Angle : 0.713 13.744 21046 Z= 0.405 Chirality : 0.042 0.189 2494 Planarity : 0.004 0.046 1881 Dihedral : 28.605 177.946 4122 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 1.53 (0.23), residues: 1311 helix: 1.46 (0.19), residues: 756 sheet: 0.21 (0.45), residues: 134 loop : 0.71 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.009 0.001 HIS F 75 PHE 0.026 0.002 PHE B 61 TYR 0.025 0.002 TYR A 99 ARG 0.006 0.000 ARG E 42 ********************** 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 203 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.266 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: 10 residues processed: 196 average time/residue: 0.2088 time to fit residues: 63.9156 Evaluate side-chains 193 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 50.0000 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 50.0000 chunk 51 optimal weight: 0.8980 chunk 126 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.077433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.055267 restraints weight = 123206.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.056220 restraints weight = 58836.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.057190 restraints weight = 37589.292| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14700 Z= 0.216 Angle : 0.719 16.019 21046 Z= 0.400 Chirality : 0.041 0.226 2494 Planarity : 0.004 0.051 1881 Dihedral : 28.248 178.099 4122 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.88 % Allowed : 30.99 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.23), residues: 1311 helix: 1.36 (0.19), residues: 768 sheet: 0.39 (0.45), residues: 134 loop : 0.70 (0.32), residues: 409 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 0.038 0.002 PHE E 104 TYR 0.022 0.002 TYR A 99 ARG 0.006 0.000 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.19 seconds wall clock time: 60 minutes 46.66 seconds (3646.66 seconds total)