Starting phenix.real_space_refine on Tue Jun 24 11:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlj_25989/06_2025/7tlj_25989_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlj_25989/06_2025/7tlj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tlj_25989/06_2025/7tlj_25989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlj_25989/06_2025/7tlj_25989.map" model { file = "/net/cci-nas-00/data/ceres_data/7tlj_25989/06_2025/7tlj_25989_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlj_25989/06_2025/7tlj_25989_trim.cif" } resolution = 2.91 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= 0.007 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.75, per 1000 atoms: 0.53 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: 8.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.85 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: 9.58 Time building geometry restraints manager: 9.66 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 430 or resid 1001 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: 12.320 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: 0.450 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 71.210 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.500 ------------------------------------------------------------------------------- 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 : 3.99 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 (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: 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 TRP 0.013 0.001 TRP A 157 HIS 0.007 0.001 HIS E 111 PHE 0.021 0.002 PHE E 216 TYR 0.010 0.001 TYR E 399 ARG 0.006 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.12928 ( 751) hydrogen bonds : angle 5.40835 ( 2142) metal coordination : bond 0.03357 ( 8) metal coordination : angle 10.27948 ( 6) SS BOND : bond 0.00538 ( 4) SS BOND : angle 1.61245 ( 8) covalent geometry : bond 0.00693 (14732) covalent geometry : angle 0.76997 (20182) 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 : 2.147 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: A 278 ASP cc_start: 0.8006 (m-30) cc_final: 0.7745 (m-30) outliers start: 19 outliers final: 3 residues processed: 242 average time/residue: 2.4580 time to fit residues: 659.3178 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 : 2.185 ------------------------------------------------------------------------------- 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 145 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.080402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.068914 restraints weight = 93063.173| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.30 r_work: 0.2855 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.488 14754 Z= 0.163 Angle : 0.645 15.649 20196 Z= 0.278 Chirality : 0.040 0.143 2122 Planarity : 0.005 0.047 2544 Dihedral : 11.553 173.841 2096 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 0.78 % Allowed : 11.57 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.06 (0.20), residues: 1758 helix: 1.61 (0.17), residues: 928 sheet: -1.36 (0.56), residues: 84 loop : -0.12 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.008 0.001 HIS E 276 PHE 0.021 0.001 PHE E 216 TYR 0.011 0.001 TYR A 399 ARG 0.003 0.000 ARG F 48 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 751) hydrogen bonds : angle 4.40620 ( 2142) metal coordination : bond 0.00906 ( 8) metal coordination : angle 8.35250 ( 6) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.54548 ( 8) covalent geometry : bond 0.00368 (14732) covalent geometry : angle 0.62900 (20182) Misc. bond : bond 0.27907 ( 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: 11 poor density : 157 time to evaluate : 1.998 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: 0.8355 (mm-40) cc_final: 0.7992 (mm-40) REVERT: E 276 HIS cc_start: 0.8766 (t70) cc_final: 0.8474 (t-170) REVERT: F 140 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8969 (tp30) REVERT: G 99 ARG cc_start: 0.8445 (mmt90) cc_final: 0.8056 (mmt90) outliers start: 11 outliers final: 4 residues processed: 165 average time/residue: 2.8899 time to fit residues: 532.3128 Evaluate side-chains 146 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 PHE 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 114 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 165 optimal weight: 0.0570 chunk 93 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3212 r_free = 0.3212 target = 0.081094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069676 restraints weight = 93045.573| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.33 r_work: 0.2878 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.364 14754 Z= 0.113 Angle : 0.547 12.560 20196 Z= 0.247 Chirality : 0.039 0.151 2122 Planarity : 0.004 0.040 2544 Dihedral : 10.346 88.233 2092 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 0.56 % Allowed : 12.13 % 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 (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: 1.40 (0.21), residues: 1758 helix: 1.92 (0.17), residues: 930 sheet: -1.28 (0.57), residues: 84 loop : 0.00 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.007 0.001 HIS E 276 PHE 0.020 0.001 PHE A 216 TYR 0.009 0.001 TYR E 399 ARG 0.002 0.000 ARG F 48 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 751) hydrogen bonds : angle 4.08985 ( 2142) metal coordination : bond 0.00555 ( 8) metal coordination : angle 7.59583 ( 6) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.66787 ( 8) covalent geometry : bond 0.00271 (14732) covalent geometry : angle 0.53104 (20182) Misc. bond : bond 0.17154 ( 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 173 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 5.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7945 (mm-40) REVERT: B 185 MET cc_start: 0.8963 (ttp) cc_final: 0.8338 (ttm) REVERT: C 79 GLU cc_start: 0.8950 (mp0) cc_final: 0.8576 (tp30) REVERT: C 99 ARG cc_start: 0.8330 (mpt180) cc_final: 0.8055 (mmt-90) REVERT: G 97 ASN cc_start: 0.8477 (t0) cc_final: 0.7972 (t0) REVERT: H 85 LEU cc_start: 0.8382 (tp) cc_final: 0.8099 (mm) outliers start: 8 outliers final: 3 residues processed: 171 average time/residue: 2.6620 time to fit residues: 507.0407 Evaluate side-chains 152 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 VAL 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 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 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 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 = 0.3191 r_free = 0.3191 target = 0.079882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068455 restraints weight = 94291.211| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.31 r_work: 0.2857 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.366 14754 Z= 0.142 Angle : 0.566 12.306 20196 Z= 0.251 Chirality : 0.039 0.145 2122 Planarity : 0.004 0.039 2544 Dihedral : 10.932 179.050 2091 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.78 % Allowed : 11.92 % 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 (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: 1.56 (0.21), residues: 1758 helix: 2.07 (0.17), residues: 930 sheet: -1.26 (0.57), residues: 84 loop : 0.05 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 157 HIS 0.007 0.001 HIS E 276 PHE 0.021 0.001 PHE A 216 TYR 0.011 0.001 TYR A 399 ARG 0.002 0.000 ARG F 48 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 751) hydrogen bonds : angle 4.01164 ( 2142) metal coordination : bond 0.00695 ( 8) metal coordination : angle 7.50035 ( 6) SS BOND : bond 0.00303 ( 4) SS BOND : angle 0.81289 ( 8) covalent geometry : bond 0.00348 (14732) covalent geometry : angle 0.55128 (20182) Misc. bond : bond 0.17146 ( 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 156 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 2.383 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 145 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9183 (mtp) REVERT: B 231 PHE cc_start: 0.8617 (m-80) cc_final: 0.7878 (t80) REVERT: C 79 GLU cc_start: 0.8960 (mp0) cc_final: 0.8580 (tp30) REVERT: C 99 ARG cc_start: 0.8413 (mpt180) cc_final: 0.8160 (mmt-90) REVERT: G 97 ASN cc_start: 0.8498 (t0) cc_final: 0.8015 (t0) REVERT: G 164 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7829 (ttpp) REVERT: G 181 GLU cc_start: 0.8841 (mp0) cc_final: 0.8614 (mp0) REVERT: H 85 LEU cc_start: 0.8456 (tp) cc_final: 0.8179 (mm) outliers start: 11 outliers final: 3 residues processed: 153 average time/residue: 3.1507 time to fit residues: 537.0167 Evaluate side-chains 155 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 6.042 ------------------------------------------------------------------------------- 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 G residue 72 ILE Chi-restraints excluded: chain G residue 164 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068836 restraints weight = 93306.430| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.30 r_work: 0.2864 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.328 14754 Z= 0.118 Angle : 0.548 11.778 20196 Z= 0.245 Chirality : 0.039 0.149 2122 Planarity : 0.004 0.037 2544 Dihedral : 9.996 88.435 2088 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 0.85 % Allowed : 11.71 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.65 (0.21), residues: 1758 helix: 2.19 (0.17), residues: 928 sheet: -1.18 (0.58), residues: 84 loop : 0.02 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 PHE 0.021 0.001 PHE A 216 TYR 0.010 0.001 TYR A 399 ARG 0.002 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 751) hydrogen bonds : angle 3.90374 ( 2142) metal coordination : bond 0.00665 ( 8) metal coordination : angle 7.31260 ( 6) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.55774 ( 8) covalent geometry : bond 0.00296 (14732) covalent geometry : angle 0.53347 (20182) Misc. bond : bond 0.15243 ( 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 165 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 2.422 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: 0.9588 (OUTLIER) cc_final: 0.9143 (mtp) REVERT: A 384 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8046 (mm-40) REVERT: B 231 PHE cc_start: 0.8628 (m-80) cc_final: 0.7905 (t80) REVERT: C 79 GLU cc_start: 0.8982 (mp0) cc_final: 0.8568 (tp30) REVERT: C 99 ARG cc_start: 0.8415 (mpt180) cc_final: 0.8190 (mmt-90) REVERT: G 97 ASN cc_start: 0.8442 (t0) cc_final: 0.7947 (t0) REVERT: H 85 LEU cc_start: 0.8449 (tp) cc_final: 0.8189 (mm) outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 2.8933 time to fit residues: 524.0075 Evaluate side-chains 149 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.068374 restraints weight = 94379.438| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.31 r_work: 0.2851 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.325 14754 Z= 0.131 Angle : 0.554 11.899 20196 Z= 0.248 Chirality : 0.039 0.147 2122 Planarity : 0.004 0.037 2544 Dihedral : 9.904 87.159 2088 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 0.71 % Allowed : 11.85 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.21), residues: 1758 helix: 2.26 (0.17), residues: 928 sheet: -1.09 (0.59), residues: 84 loop : 0.05 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 PHE 0.022 0.001 PHE A 216 TYR 0.011 0.001 TYR A 399 ARG 0.002 0.000 ARG F 48 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 751) hydrogen bonds : angle 3.85826 ( 2142) metal coordination : bond 0.00814 ( 8) metal coordination : angle 7.19036 ( 6) SS BOND : bond 0.00398 ( 4) SS BOND : angle 1.02025 ( 8) covalent geometry : bond 0.00329 (14732) covalent geometry : angle 0.54007 (20182) Misc. bond : bond 0.15287 ( 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 156 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 2.017 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: 0.8352 (mm-40) cc_final: 0.8073 (mm-40) REVERT: B 231 PHE cc_start: 0.8641 (m-80) cc_final: 0.7945 (t80) REVERT: C 79 GLU cc_start: 0.8978 (mp0) cc_final: 0.8525 (tp30) REVERT: E 276 HIS cc_start: 0.8717 (t70) cc_final: 0.8213 (t-170) REVERT: G 97 ASN cc_start: 0.8441 (t0) cc_final: 0.7925 (t0) REVERT: G 181 GLU cc_start: 0.8853 (mp0) cc_final: 0.8595 (mp0) REVERT: H 85 LEU cc_start: 0.8483 (tp) cc_final: 0.8225 (mm) outliers start: 10 outliers final: 5 residues processed: 153 average time/residue: 2.6665 time to fit residues: 451.5927 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 : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 191 ASP 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 23 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 139 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.067333 restraints weight = 94534.818| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.28 r_work: 0.2836 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.339 14754 Z= 0.158 Angle : 0.573 12.436 20196 Z= 0.255 Chirality : 0.039 0.146 2122 Planarity : 0.004 0.038 2544 Dihedral : 9.829 87.113 2088 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.33 % 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 (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: 1.79 (0.21), residues: 1758 helix: 2.29 (0.17), residues: 928 sheet: -0.94 (0.61), residues: 84 loop : 0.09 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 PHE 0.022 0.001 PHE A 216 TYR 0.012 0.001 TYR A 399 ARG 0.002 0.000 ARG E 355 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 751) hydrogen bonds : angle 3.86607 ( 2142) metal coordination : bond 0.01036 ( 8) metal coordination : angle 7.16340 ( 6) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.78981 ( 8) covalent geometry : bond 0.00392 (14732) covalent geometry : angle 0.55944 (20182) Misc. bond : bond 0.16619 ( 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 152 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 4.010 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: 0.8392 (mm-40) cc_final: 0.8123 (mm-40) REVERT: B 231 PHE cc_start: 0.8628 (m-80) cc_final: 0.7925 (t80) REVERT: C 79 GLU cc_start: 0.8976 (mp0) cc_final: 0.8529 (tp30) REVERT: G 181 GLU cc_start: 0.8883 (mp0) cc_final: 0.8613 (mp0) REVERT: H 85 LEU cc_start: 0.8481 (tp) cc_final: 0.8219 (mm) outliers start: 9 outliers final: 4 residues processed: 149 average time/residue: 3.8087 time to fit residues: 636.0715 Evaluate side-chains 141 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 114 MET 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 117 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068296 restraints weight = 93968.180| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.28 r_work: 0.2858 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.305 14754 Z= 0.117 Angle : 0.556 12.085 20196 Z= 0.251 Chirality : 0.039 0.149 2122 Planarity : 0.004 0.038 2544 Dihedral : 9.675 88.391 2088 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 0.63 % Allowed : 12.13 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.84 (0.21), residues: 1758 helix: 2.32 (0.17), residues: 928 sheet: -0.88 (0.61), residues: 84 loop : 0.13 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 PHE 0.021 0.001 PHE A 216 TYR 0.010 0.001 TYR A 399 ARG 0.002 0.000 ARG F 81 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 751) hydrogen bonds : angle 3.80942 ( 2142) metal coordination : bond 0.00788 ( 8) metal coordination : angle 6.98546 ( 6) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.58081 ( 8) covalent geometry : bond 0.00302 (14732) covalent geometry : angle 0.54244 (20182) Misc. bond : bond 0.14510 ( 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 164 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.827 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: 0.9561 (OUTLIER) cc_final: 0.9152 (mtp) REVERT: A 384 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8113 (mm-40) REVERT: B 231 PHE cc_start: 0.8619 (m-80) cc_final: 0.7938 (t80) REVERT: C 79 GLU cc_start: 0.8960 (mp0) cc_final: 0.8522 (tp30) REVERT: G 181 GLU cc_start: 0.8897 (mp0) cc_final: 0.8620 (mp0) REVERT: H 85 LEU cc_start: 0.8506 (tp) cc_final: 0.8246 (mm) outliers start: 9 outliers final: 3 residues processed: 162 average time/residue: 2.8632 time to fit residues: 516.0175 Evaluate side-chains 146 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 G residue 72 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 0.0050 chunk 97 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068132 restraints weight = 94820.038| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.29 r_work: 0.2856 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.291 14754 Z= 0.120 Angle : 0.552 11.979 20196 Z= 0.249 Chirality : 0.039 0.151 2122 Planarity : 0.004 0.038 2544 Dihedral : 9.568 89.358 2088 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 0.56 % Allowed : 12.69 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.88 (0.21), residues: 1758 helix: 2.36 (0.17), residues: 928 sheet: -0.86 (0.62), residues: 84 loop : 0.14 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.005 0.001 HIS E 276 PHE 0.021 0.001 PHE A 216 TYR 0.010 0.001 TYR A 399 ARG 0.005 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 751) hydrogen bonds : angle 3.78710 ( 2142) metal coordination : bond 0.00848 ( 8) metal coordination : angle 6.88042 ( 6) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.49989 ( 8) covalent geometry : bond 0.00309 (14732) covalent geometry : angle 0.53892 (20182) Misc. bond : bond 0.14055 ( 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 151 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.938 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: 0.9556 (OUTLIER) cc_final: 0.9166 (mtp) REVERT: A 384 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8132 (mm-40) REVERT: B 231 PHE cc_start: 0.8629 (m-80) cc_final: 0.7985 (t80) REVERT: C 79 GLU cc_start: 0.8977 (mp0) cc_final: 0.8532 (tp30) REVERT: E 276 HIS cc_start: 0.8640 (t-90) cc_final: 0.8262 (t-170) REVERT: G 181 GLU cc_start: 0.8895 (mp0) cc_final: 0.8633 (mp0) REVERT: H 85 LEU cc_start: 0.8496 (tp) cc_final: 0.8243 (mm) outliers start: 8 outliers final: 4 residues processed: 149 average time/residue: 2.4569 time to fit residues: 405.7170 Evaluate side-chains 145 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 114 MET 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 40 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 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** B 5 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.068536 restraints weight = 94308.821| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.30 r_work: 0.2849 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 14754 Z= 0.112 Angle : 0.557 11.955 20196 Z= 0.253 Chirality : 0.039 0.152 2122 Planarity : 0.004 0.037 2544 Dihedral : 9.464 89.613 2088 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 0.21 % Allowed : 13.12 % 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 (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: 1.90 (0.21), residues: 1758 helix: 2.38 (0.17), residues: 930 sheet: -0.86 (0.62), residues: 84 loop : 0.13 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 157 HIS 0.005 0.001 HIS B 5 PHE 0.021 0.001 PHE A 216 TYR 0.010 0.001 TYR A 399 ARG 0.005 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 751) hydrogen bonds : angle 3.75434 ( 2142) metal coordination : bond 0.00795 ( 8) metal coordination : angle 6.77745 ( 6) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.65617 ( 8) covalent geometry : bond 0.00290 (14732) covalent geometry : angle 0.54509 (20182) Misc. bond : bond 0.13120 ( 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 147 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 2.013 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: 0.8405 (mm-40) cc_final: 0.8134 (mm-40) REVERT: B 231 PHE cc_start: 0.8631 (m-80) cc_final: 0.7970 (t80) REVERT: C 79 GLU cc_start: 0.8990 (mp0) cc_final: 0.8530 (tp30) REVERT: C 89 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7818 (mm110) REVERT: E 276 HIS cc_start: 0.8739 (t-90) cc_final: 0.8491 (t70) REVERT: G 181 GLU cc_start: 0.8904 (mp0) cc_final: 0.8636 (mp0) REVERT: H 85 LEU cc_start: 0.8473 (tp) cc_final: 0.8225 (mm) outliers start: 3 outliers final: 3 residues processed: 147 average time/residue: 2.8031 time to fit residues: 456.1160 Evaluate side-chains 144 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 63 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 136 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.068490 restraints weight = 94585.567| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.27 r_work: 0.2857 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 14754 Z= 0.116 Angle : 0.550 12.392 20196 Z= 0.247 Chirality : 0.039 0.150 2122 Planarity : 0.004 0.036 2544 Dihedral : 9.390 89.031 2088 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 0.63 % Allowed : 12.62 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.95 (0.21), residues: 1758 helix: 2.42 (0.17), residues: 928 sheet: -0.85 (0.62), residues: 84 loop : 0.15 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.005 0.001 HIS B 5 PHE 0.020 0.001 PHE A 216 TYR 0.010 0.001 TYR A 399 ARG 0.004 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 751) hydrogen bonds : angle 3.73724 ( 2142) metal coordination : bond 0.00858 ( 8) metal coordination : angle 6.77095 ( 6) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.58746 ( 8) covalent geometry : bond 0.00301 (14732) covalent geometry : angle 0.53785 (20182) Misc. bond : bond 0.13239 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17437.72 seconds wall clock time: 307 minutes 11.58 seconds (18431.58 seconds total)