Starting phenix.real_space_refine on Fri Mar 6 05:05:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlj_25989/03_2026/7tlj_25989_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlj_25989/03_2026/7tlj_25989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tlj_25989/03_2026/7tlj_25989_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlj_25989/03_2026/7tlj_25989_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tlj_25989/03_2026/7tlj_25989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlj_25989/03_2026/7tlj_25989.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.277 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: 7 Type Number sf(0) Gaussians Fe 10 7.16 5 P 2 5.49 5 S 72 5.16 5 C 9378 2.51 5 N 2312 2.21 5 O 2468 1.98 5 H 13511 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27753 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6850 Classifications: {'peptide': 428} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 399} Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 3794 Classifications: {'peptide': 256} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 235} Chain: "C" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2648 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 378 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "E" Number of atoms: 6851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6851 Classifications: {'peptide': 428} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 399} Chain: "F" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 3794 Classifications: {'peptide': 256} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 235} Chain: "G" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2648 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 378 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'HEM': 2, 'LOP': 1, 'PQU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'HEM': 2, 'LOP': 1, 'PQU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12451 SG CYS C 129 60.107 26.204 68.142 1.00 62.25 S ATOM 12715 SG CYS C 149 56.545 26.275 68.783 1.00 57.81 S ATOM 26122 SG CYS G 129 44.451 88.466 68.175 1.00 69.88 S ATOM 26386 SG CYS G 149 47.890 88.169 69.125 1.00 64.04 S Time building chain proxies: 5.12, per 1000 atoms: 0.18 Number of scatterers: 27753 At special positions: 0 Unit cell: (106.24, 115.37, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 10 26.01 S 72 16.00 P 2 15.00 O 2468 8.00 N 2312 7.00 C 9378 6.00 H 13511 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 151 " distance=2.03 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 745.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C1001 " pdb="FE2 FES C1001 " - pdb=" ND1 HIS C 152 " pdb="FE2 FES C1001 " - pdb=" ND1 HIS C 131 " pdb="FE1 FES C1001 " - pdb=" SG CYS C 149 " pdb="FE1 FES C1001 " - pdb=" SG CYS C 129 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" ND1 HIS G 131 " pdb="FE2 FES G1001 " - pdb=" ND1 HIS G 152 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 129 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 149 " Number of angles added : 6 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3224 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 12 sheets defined 57.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.563A pdb=" N SER A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.507A pdb=" N LEU A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 67 removed outlier: 3.569A pdb=" N MET A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 89 through 118 removed outlier: 3.807A pdb=" N ALA A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 149 removed outlier: 3.719A pdb=" N LEU A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.577A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 187 through 220 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.681A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.165A pdb=" N PHE A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 327 through 345 removed outlier: 3.887A pdb=" N ILE A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.545A pdb=" N LEU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.759A pdb=" N TYR A 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 382 removed outlier: 3.639A pdb=" N TYR A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.886A pdb=" N PHE A 404 " --> pdb=" O TRP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.718A pdb=" N ALA A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.521A pdb=" N ASP A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 36 through 39 Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 59 through 68 removed outlier: 3.610A pdb=" N THR B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 203 through 220 Processing helix chain 'B' and resid 222 through 256 removed outlier: 3.983A pdb=" N GLY B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 37 Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.917A pdb=" N VAL C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.862A pdb=" N THR C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 100 Processing helix chain 'E' and resid 13 through 21 removed outlier: 3.524A pdb=" N SER E 21 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 46 through 67 removed outlier: 3.565A pdb=" N MET E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 89 through 119 removed outlier: 3.822A pdb=" N ALA E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 149 Processing helix chain 'E' and resid 152 through 168 Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 187 through 220 Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 233 through 240 Processing helix chain 'E' and resid 246 through 270 Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 298 through 308 removed outlier: 4.230A pdb=" N PHE E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 327 through 350 removed outlier: 3.901A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix Processing helix chain 'E' and resid 356 through 359 removed outlier: 3.613A pdb=" N TYR E 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 360 through 382 removed outlier: 3.851A pdb=" N ILE E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA E 382 " --> pdb=" O THR E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.936A pdb=" N PHE E 404 " --> pdb=" O TRP E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 415 removed outlier: 3.681A pdb=" N ALA E 413 " --> pdb=" O PRO E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 429 removed outlier: 3.562A pdb=" N ASP E 427 " --> pdb=" O THR E 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 35 Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.710A pdb=" N GLN F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 removed outlier: 3.543A pdb=" N ARG F 107 " --> pdb=" O MET F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 126 through 136 Processing helix chain 'F' and resid 143 through 147 removed outlier: 3.551A pdb=" N GLU F 147 " --> pdb=" O LYS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'F' and resid 203 through 220 Processing helix chain 'F' and resid 222 through 253 Processing helix chain 'G' and resid 11 through 37 removed outlier: 3.536A pdb=" N LEU G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 78 through 88 Processing helix chain 'G' and resid 110 through 114 Processing helix chain 'H' and resid 81 through 100 removed outlier: 3.593A pdb=" N PHE H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AA3, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.781A pdb=" N GLY C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 146 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'F' and resid 71 through 73 Processing sheet with id=AA9, first strand: chain 'F' and resid 155 through 157 Processing sheet with id=AB1, first strand: chain 'G' and resid 50 through 53 removed outlier: 6.420A pdb=" N THR G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 62 through 67 Processing sheet with id=AB3, first strand: chain 'G' and resid 137 through 141 removed outlier: 4.574A pdb=" N GLY G 139 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY G 146 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 164 " --> pdb=" O HIS G 155 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 13509 1.11 - 1.39: 6108 1.39 - 1.66: 8470 1.66 - 1.93: 124 1.93 - 2.21: 32 Bond restraints: 28243 Sorted by residual: bond pdb=" O4 LOP A1004 " pdb=" P1 LOP A1004 " ideal model delta sigma weight residual 1.500 1.720 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O4 LOP E1004 " pdb=" P1 LOP E1004 " ideal model delta sigma weight residual 1.500 1.720 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O3 LOP A1004 " pdb=" P1 LOP A1004 " ideal model delta sigma weight residual 1.497 1.714 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" O3 LOP E1004 " pdb=" P1 LOP E1004 " ideal model delta sigma weight residual 1.497 1.714 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O2 LOP A1004 " pdb=" P1 LOP A1004 " ideal model delta sigma weight residual 1.650 1.542 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 28238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 50349 2.36 - 4.73: 446 4.73 - 7.09: 58 7.09 - 9.45: 11 9.45 - 11.81: 8 Bond angle restraints: 50872 Sorted by residual: angle pdb=" CG ARG G 99 " pdb=" CD ARG G 99 " pdb=" NE ARG G 99 " ideal model delta sigma weight residual 112.00 122.22 -10.22 2.20e+00 2.07e-01 2.16e+01 angle pdb=" O2 LOP A1004 " pdb=" P1 LOP A1004 " pdb=" O3 LOP A1004 " ideal model delta sigma weight residual 110.20 98.39 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O2 LOP E1004 " pdb=" P1 LOP E1004 " pdb=" O3 LOP E1004 " ideal model delta sigma weight residual 110.20 99.10 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O1 LOP A1004 " pdb=" P1 LOP A1004 " pdb=" O3 LOP A1004 " ideal model delta sigma weight residual 106.68 117.42 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1 LOP E1004 " pdb=" P1 LOP E1004 " pdb=" O3 LOP E1004 " ideal model delta sigma weight residual 106.68 116.93 -10.25 3.00e+00 1.11e-01 1.17e+01 ... (remaining 50867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12108 17.98 - 35.97: 810 35.97 - 53.95: 358 53.95 - 71.94: 116 71.94 - 89.92: 21 Dihedral angle restraints: 13413 sinusoidal: 7068 harmonic: 6345 Sorted by residual: dihedral pdb=" CG ARG G 99 " pdb=" CD ARG G 99 " pdb=" NE ARG G 99 " pdb=" CZ ARG G 99 " ideal model delta sinusoidal sigma weight residual 90.00 31.87 58.13 2 1.50e+01 4.44e-03 1.54e+01 dihedral pdb=" C2D HEC F1001 " pdb=" C3D HEC F1001 " pdb=" CAD HEC F1001 " pdb=" CBD HEC F1001 " ideal model delta sinusoidal sigma weight residual 0.00 89.92 -89.92 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C3D HEM A1001 " pdb=" CAD HEM A1001 " pdb=" CBD HEM A1001 " pdb=" CGD HEM A1001 " ideal model delta sinusoidal sigma weight residual 180.00 90.89 89.11 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2048 0.100 - 0.201: 72 0.201 - 0.301: 0 0.301 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 2122 Sorted by residual: chirality pdb=" C4 LOP A1004 " pdb=" C3 LOP A1004 " pdb=" C5 LOP A1004 " pdb=" O5 LOP A1004 " both_signs ideal model delta sigma weight residual False -2.34 -1.84 -0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" C4 LOP E1004 " pdb=" C3 LOP E1004 " pdb=" C5 LOP E1004 " pdb=" O5 LOP E1004 " both_signs ideal model delta sigma weight residual False -2.34 -1.98 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ILE G 74 " pdb=" N ILE G 74 " pdb=" C ILE G 74 " pdb=" CB ILE G 74 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 2119 not shown) Planarity restraints: 4192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP E1004 " 0.080 2.00e-02 2.50e+03 1.50e-01 2.24e+02 pdb=" C14 LOP E1004 " -0.196 2.00e-02 2.50e+03 pdb=" C15 LOP E1004 " 0.196 2.00e-02 2.50e+03 pdb=" C16 LOP E1004 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 LOP E1004 " -0.121 2.00e-02 2.50e+03 6.99e-02 4.89e+01 pdb=" C7 LOP E1004 " 0.035 2.00e-02 2.50e+03 pdb=" O5 LOP E1004 " 0.043 2.00e-02 2.50e+03 pdb=" O7 LOP E1004 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC B1001 " 0.008 2.00e-02 2.50e+03 4.33e-02 4.22e+01 pdb=" C2C HEC B1001 " -0.116 2.00e-02 2.50e+03 pdb=" C3C HEC B1001 " 0.039 2.00e-02 2.50e+03 pdb=" C4C HEC B1001 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC B1001 " 0.008 2.00e-02 2.50e+03 pdb=" CHC HEC B1001 " 0.022 2.00e-02 2.50e+03 pdb=" CHD HEC B1001 " -0.002 2.00e-02 2.50e+03 pdb=" CMC HEC B1001 " 0.036 2.00e-02 2.50e+03 pdb=" NC HEC B1001 " -0.001 2.00e-02 2.50e+03 ... (remaining 4189 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3051 2.25 - 2.84: 60417 2.84 - 3.42: 74202 3.42 - 4.01: 102585 4.01 - 4.60: 157751 Nonbonded interactions: 398006 Sorted by model distance: nonbonded pdb="HH12 ARG E 114 " pdb=" O2A HEM E1002 " model vdw 1.662 2.450 nonbonded pdb="HH22 ARG E 85 " pdb=" O ALA F 218 " model vdw 1.677 2.450 nonbonded pdb="HH12 ARG A 114 " pdb=" O2A HEM A1002 " model vdw 1.686 2.450 nonbonded pdb=" O CYS F 169 " pdb=" HG1 THR F 177 " model vdw 1.696 2.450 nonbonded pdb=" O ALA B 65 " pdb=" HG1 THR B 68 " model vdw 1.707 2.450 ... (remaining 398001 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' and (resid 3 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 98 through 1004)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.770 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.220 14754 Z= 0.316 Angle : 0.790 18.571 20196 Z= 0.357 Chirality : 0.044 0.501 2122 Planarity : 0.006 0.150 2544 Dihedral : 14.127 89.920 5118 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.34 % Allowed : 7.55 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1758 helix: 1.01 (0.17), residues: 926 sheet: -1.76 (0.54), residues: 84 loop : -0.57 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 99 TYR 0.010 0.001 TYR E 399 PHE 0.021 0.002 PHE E 216 TRP 0.013 0.001 TRP A 157 HIS 0.007 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00693 (14732) covalent geometry : angle 0.76997 (20182) SS BOND : bond 0.00538 ( 4) SS BOND : angle 1.61245 ( 8) hydrogen bonds : bond 0.12928 ( 751) hydrogen bonds : angle 5.40835 ( 2142) metal coordination : bond 0.03357 ( 8) metal coordination : angle 10.27948 ( 6) Misc. bond : bond 0.11975 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.704 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 outliers start: 19 outliers final: 3 residues processed: 242 average time/residue: 1.2935 time to fit residues: 344.3733 Evaluate side-chains 153 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 173 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069850 restraints weight = 92591.700| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.29 r_work: 0.2871 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.428 14754 Z= 0.133 Angle : 0.597 13.016 20196 Z= 0.268 Chirality : 0.040 0.151 2122 Planarity : 0.005 0.047 2544 Dihedral : 11.512 174.203 2096 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 0.71 % Allowed : 11.57 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1758 helix: 1.63 (0.17), residues: 928 sheet: -1.33 (0.56), residues: 84 loop : -0.09 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.010 0.001 TYR A 399 PHE 0.020 0.001 PHE E 216 TRP 0.011 0.001 TRP A 157 HIS 0.009 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00309 (14732) covalent geometry : angle 0.57950 (20182) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.55541 ( 8) hydrogen bonds : bond 0.04622 ( 751) hydrogen bonds : angle 4.34318 ( 2142) metal coordination : bond 0.00848 ( 8) metal coordination : angle 8.24639 ( 6) Misc. bond : bond 0.23350 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.769 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: A 384 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7947 (mm-40) REVERT: E 276 HIS cc_start: 0.8774 (t70) cc_final: 0.8481 (t-170) REVERT: F 140 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8968 (tp30) REVERT: G 99 ARG cc_start: 0.8407 (mmt90) cc_final: 0.8033 (mmt90) outliers start: 10 outliers final: 4 residues processed: 166 average time/residue: 1.3651 time to fit residues: 248.0955 Evaluate side-chains 153 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.069702 restraints weight = 93461.638| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.29 r_work: 0.2882 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.377 14754 Z= 0.114 Angle : 0.554 12.501 20196 Z= 0.248 Chirality : 0.039 0.150 2122 Planarity : 0.004 0.039 2544 Dihedral : 10.416 88.393 2092 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.22 % Favored : 97.72 % Rotamer: Outliers : 0.63 % Allowed : 12.06 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1758 helix: 1.93 (0.17), residues: 928 sheet: -1.27 (0.57), residues: 84 loop : 0.02 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 48 TYR 0.010 0.001 TYR H 83 PHE 0.019 0.001 PHE A 216 TRP 0.012 0.001 TRP A 157 HIS 0.007 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00276 (14732) covalent geometry : angle 0.53823 (20182) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.52181 ( 8) hydrogen bonds : bond 0.04262 ( 751) hydrogen bonds : angle 4.10730 ( 2142) metal coordination : bond 0.00575 ( 8) metal coordination : angle 7.59816 ( 6) Misc. bond : bond 0.17534 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.743 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: B 185 MET cc_start: 0.9152 (ttp) cc_final: 0.8507 (ttp) REVERT: C 79 GLU cc_start: 0.8913 (mp0) cc_final: 0.8601 (tp30) REVERT: C 99 ARG cc_start: 0.8308 (mmt90) cc_final: 0.8067 (mmt90) REVERT: E 276 HIS cc_start: 0.8718 (t70) cc_final: 0.8199 (t-170) REVERT: F 140 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.9002 (tp30) REVERT: G 97 ASN cc_start: 0.8553 (t0) cc_final: 0.8054 (t0) REVERT: H 85 LEU cc_start: 0.8427 (tp) cc_final: 0.8128 (mm) outliers start: 9 outliers final: 5 residues processed: 177 average time/residue: 1.3140 time to fit residues: 255.8948 Evaluate side-chains 156 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.067218 restraints weight = 94081.154| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.27 r_work: 0.2828 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.401 14754 Z= 0.192 Angle : 0.599 13.150 20196 Z= 0.265 Chirality : 0.040 0.143 2122 Planarity : 0.004 0.040 2544 Dihedral : 11.024 179.483 2091 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 0.99 % Allowed : 11.71 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1758 helix: 2.04 (0.17), residues: 930 sheet: -1.29 (0.58), residues: 84 loop : 0.04 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 75 TYR 0.013 0.001 TYR A 399 PHE 0.022 0.001 PHE A 216 TRP 0.009 0.001 TRP A 157 HIS 0.007 0.001 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00462 (14732) covalent geometry : angle 0.58469 (20182) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.71259 ( 8) hydrogen bonds : bond 0.04308 ( 751) hydrogen bonds : angle 4.07221 ( 2142) metal coordination : bond 0.01019 ( 8) metal coordination : angle 7.63083 ( 6) Misc. bond : bond 0.19565 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.670 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 384 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8095 (mm-40) REVERT: C 79 GLU cc_start: 0.8967 (mp0) cc_final: 0.8601 (tp30) REVERT: E 276 HIS cc_start: 0.8735 (t70) cc_final: 0.8343 (t-170) REVERT: F 140 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8983 (tp30) REVERT: G 99 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8124 (mmt90) REVERT: G 164 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7844 (tmmt) outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 1.4055 time to fit residues: 243.4314 Evaluate side-chains 150 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.067574 restraints weight = 94039.683| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.29 r_work: 0.2837 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.367 14754 Z= 0.142 Angle : 0.563 12.389 20196 Z= 0.252 Chirality : 0.039 0.147 2122 Planarity : 0.004 0.039 2544 Dihedral : 10.144 89.347 2091 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 0.85 % Allowed : 12.27 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1758 helix: 2.13 (0.17), residues: 928 sheet: -1.21 (0.58), residues: 84 loop : -0.01 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 355 TYR 0.011 0.001 TYR E 399 PHE 0.022 0.001 PHE A 216 TRP 0.011 0.001 TRP E 157 HIS 0.007 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00353 (14732) covalent geometry : angle 0.54829 (20182) SS BOND : bond 0.00381 ( 4) SS BOND : angle 0.50665 ( 8) hydrogen bonds : bond 0.04138 ( 751) hydrogen bonds : angle 3.98317 ( 2142) metal coordination : bond 0.00891 ( 8) metal coordination : angle 7.48108 ( 6) Misc. bond : bond 0.17292 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.9176 (mtp) REVERT: A 384 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8117 (mm-40) REVERT: C 79 GLU cc_start: 0.8980 (mp0) cc_final: 0.8613 (tp30) REVERT: F 140 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8983 (tp30) REVERT: G 97 ASN cc_start: 0.8445 (t0) cc_final: 0.7905 (t0) outliers start: 12 outliers final: 3 residues processed: 157 average time/residue: 1.3934 time to fit residues: 240.1365 Evaluate side-chains 148 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN B 5 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068126 restraints weight = 93921.254| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.29 r_work: 0.2848 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.335 14754 Z= 0.121 Angle : 0.557 12.048 20196 Z= 0.252 Chirality : 0.039 0.149 2122 Planarity : 0.004 0.037 2544 Dihedral : 9.966 86.804 2088 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 0.85 % Allowed : 12.13 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.21), residues: 1758 helix: 2.22 (0.17), residues: 928 sheet: -1.09 (0.59), residues: 84 loop : 0.09 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 99 TYR 0.011 0.001 TYR E 399 PHE 0.022 0.001 PHE A 216 TRP 0.011 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00306 (14732) covalent geometry : angle 0.54144 (20182) SS BOND : bond 0.00395 ( 4) SS BOND : angle 2.02274 ( 8) hydrogen bonds : bond 0.03993 ( 751) hydrogen bonds : angle 3.90127 ( 2142) metal coordination : bond 0.00775 ( 8) metal coordination : angle 7.23832 ( 6) Misc. bond : bond 0.15503 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8104 (mm-40) REVERT: C 79 GLU cc_start: 0.8974 (mp0) cc_final: 0.8583 (tp30) REVERT: G 97 ASN cc_start: 0.8430 (t0) cc_final: 0.7911 (t0) outliers start: 12 outliers final: 5 residues processed: 162 average time/residue: 1.3142 time to fit residues: 233.8115 Evaluate side-chains 150 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 119 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN B 5 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.067848 restraints weight = 93507.958| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.29 r_work: 0.2844 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 14754 Z= 0.130 Angle : 0.555 12.061 20196 Z= 0.251 Chirality : 0.039 0.148 2122 Planarity : 0.004 0.035 2544 Dihedral : 9.818 87.501 2088 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 0.78 % Allowed : 12.55 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.21), residues: 1758 helix: 2.27 (0.17), residues: 928 sheet: -0.98 (0.60), residues: 84 loop : 0.11 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 99 TYR 0.011 0.001 TYR E 399 PHE 0.022 0.001 PHE A 216 TRP 0.010 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00330 (14732) covalent geometry : angle 0.54026 (20182) SS BOND : bond 0.00342 ( 4) SS BOND : angle 1.37028 ( 8) hydrogen bonds : bond 0.03944 ( 751) hydrogen bonds : angle 3.86253 ( 2142) metal coordination : bond 0.00882 ( 8) metal coordination : angle 7.12230 ( 6) Misc. bond : bond 0.15125 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.691 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 384 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8071 (mm-40) REVERT: B 231 PHE cc_start: 0.8644 (m-80) cc_final: 0.8012 (t80) REVERT: C 79 GLU cc_start: 0.8982 (mp0) cc_final: 0.8577 (tp30) REVERT: G 97 ASN cc_start: 0.8418 (t0) cc_final: 0.7889 (t0) outliers start: 11 outliers final: 4 residues processed: 156 average time/residue: 1.2340 time to fit residues: 212.5435 Evaluate side-chains 148 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 50 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN B 5 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067901 restraints weight = 93743.414| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.30 r_work: 0.2843 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.311 14754 Z= 0.128 Angle : 0.562 12.097 20196 Z= 0.255 Chirality : 0.039 0.150 2122 Planarity : 0.004 0.035 2544 Dihedral : 9.699 88.249 2088 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 0.85 % Allowed : 11.99 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.21), residues: 1758 helix: 2.32 (0.17), residues: 928 sheet: -0.94 (0.61), residues: 84 loop : 0.17 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 81 TYR 0.011 0.001 TYR A 399 PHE 0.021 0.001 PHE A 216 TRP 0.010 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00328 (14732) covalent geometry : angle 0.54895 (20182) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.00430 ( 8) hydrogen bonds : bond 0.03893 ( 751) hydrogen bonds : angle 3.82911 ( 2142) metal coordination : bond 0.00884 ( 8) metal coordination : angle 7.00707 ( 6) Misc. bond : bond 0.14781 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.759 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 145 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9163 (mtp) REVERT: A 384 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8088 (mm-40) REVERT: B 231 PHE cc_start: 0.8631 (m-80) cc_final: 0.8000 (t80) REVERT: C 79 GLU cc_start: 0.8986 (mp0) cc_final: 0.8567 (tp30) REVERT: E 276 HIS cc_start: 0.8707 (t70) cc_final: 0.8278 (t-170) outliers start: 12 outliers final: 4 residues processed: 157 average time/residue: 1.2648 time to fit residues: 218.9785 Evaluate side-chains 147 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068584 restraints weight = 94321.363| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.33 r_work: 0.2850 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 14754 Z= 0.114 Angle : 0.551 11.880 20196 Z= 0.250 Chirality : 0.039 0.151 2122 Planarity : 0.004 0.035 2544 Dihedral : 9.570 89.448 2088 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.56 % Allowed : 12.48 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.21), residues: 1758 helix: 2.36 (0.17), residues: 928 sheet: -0.88 (0.62), residues: 84 loop : 0.17 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 81 TYR 0.010 0.001 TYR E 399 PHE 0.020 0.001 PHE A 216 TRP 0.011 0.001 TRP E 157 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00294 (14732) covalent geometry : angle 0.53750 (20182) SS BOND : bond 0.00549 ( 4) SS BOND : angle 1.55229 ( 8) hydrogen bonds : bond 0.03813 ( 751) hydrogen bonds : angle 3.77872 ( 2142) metal coordination : bond 0.00812 ( 8) metal coordination : angle 6.89304 ( 6) Misc. bond : bond 0.13686 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.638 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 145 MET cc_start: 0.9538 (OUTLIER) cc_final: 0.9138 (mtp) REVERT: A 384 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8160 (mm-40) REVERT: B 231 PHE cc_start: 0.8638 (m-80) cc_final: 0.7998 (t80) REVERT: C 79 GLU cc_start: 0.9002 (mp0) cc_final: 0.8555 (tp30) REVERT: C 99 ARG cc_start: 0.8440 (mpt180) cc_final: 0.8226 (mmt-90) REVERT: G 97 ASN cc_start: 0.8405 (t0) cc_final: 0.7954 (t0) outliers start: 8 outliers final: 4 residues processed: 156 average time/residue: 1.2665 time to fit residues: 217.7076 Evaluate side-chains 149 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 131 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.068548 restraints weight = 93887.456| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.29 r_work: 0.2862 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.270 14754 Z= 0.112 Angle : 0.561 11.923 20196 Z= 0.255 Chirality : 0.039 0.151 2122 Planarity : 0.004 0.036 2544 Dihedral : 9.459 89.516 2088 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 0.42 % Allowed : 12.62 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.21), residues: 1758 helix: 2.40 (0.17), residues: 930 sheet: -0.88 (0.62), residues: 84 loop : 0.16 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 81 TYR 0.010 0.001 TYR A 399 PHE 0.021 0.001 PHE A 216 TRP 0.011 0.001 TRP E 157 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00293 (14732) covalent geometry : angle 0.54866 (20182) SS BOND : bond 0.00485 ( 4) SS BOND : angle 1.16244 ( 8) hydrogen bonds : bond 0.03741 ( 751) hydrogen bonds : angle 3.73992 ( 2142) metal coordination : bond 0.00791 ( 8) metal coordination : angle 6.80374 ( 6) Misc. bond : bond 0.13109 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.717 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 384 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8150 (mm-40) REVERT: B 144 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8837 (tppt) REVERT: B 231 PHE cc_start: 0.8643 (m-80) cc_final: 0.8016 (t80) REVERT: C 79 GLU cc_start: 0.8997 (mp0) cc_final: 0.8544 (tp30) REVERT: C 89 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7808 (mm110) REVERT: E 276 HIS cc_start: 0.8722 (t70) cc_final: 0.8293 (t-170) REVERT: G 97 ASN cc_start: 0.8383 (t0) cc_final: 0.7960 (t0) outliers start: 6 outliers final: 3 residues processed: 151 average time/residue: 1.3018 time to fit residues: 216.5605 Evaluate side-chains 148 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN B 5 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN F 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.068606 restraints weight = 93959.950| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.29 r_work: 0.2860 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.270 14754 Z= 0.111 Angle : 0.541 12.495 20196 Z= 0.243 Chirality : 0.039 0.151 2122 Planarity : 0.004 0.048 2544 Dihedral : 9.387 89.035 2088 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 0.49 % Allowed : 12.62 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.21), residues: 1758 helix: 2.45 (0.17), residues: 928 sheet: -0.87 (0.62), residues: 84 loop : 0.18 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 81 TYR 0.010 0.001 TYR A 399 PHE 0.019 0.001 PHE A 216 TRP 0.011 0.001 TRP E 157 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00287 (14732) covalent geometry : angle 0.52820 (20182) SS BOND : bond 0.00460 ( 4) SS BOND : angle 1.10797 ( 8) hydrogen bonds : bond 0.03713 ( 751) hydrogen bonds : angle 3.71549 ( 2142) metal coordination : bond 0.00808 ( 8) metal coordination : angle 6.76458 ( 6) Misc. bond : bond 0.12966 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8123.78 seconds wall clock time: 138 minutes 2.72 seconds (8282.72 seconds total)