Starting phenix.real_space_refine on Fri Aug 22 20:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pmq_17764/08_2025/8pmq_17764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmq_17764/08_2025/8pmq_17764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pmq_17764/08_2025/8pmq_17764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmq_17764/08_2025/8pmq_17764.map" model { file = "/net/cci-nas-00/data/ceres_data/8pmq_17764/08_2025/8pmq_17764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmq_17764/08_2025/8pmq_17764.cif" } resolution = 3.53 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 30 5.16 5 C 5004 2.51 5 N 1313 2.21 5 O 1395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7746 Number of models: 1 Model: "" Number of chains: 6 Chain: "2" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2730 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "9" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3249 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 14, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 10, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1223 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "U" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 542 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2414 SG CYS 2 379 39.864 102.744 20.884 1.00 30.00 S ATOM 2586 SG CYS 2 401 36.510 100.570 20.969 1.00 29.77 S ATOM 2611 SG CYS 2 404 37.498 102.692 23.847 1.00 31.98 S ATOM 5236 SG CYS 9 395 46.973 72.158 24.507 1.00 29.24 S ATOM 5347 SG CYS 9 434 50.384 72.607 26.571 1.00 20.06 S ATOM 5367 SG CYS 9 437 50.403 71.416 23.057 1.00 20.18 S Time building chain proxies: 1.79, per 1000 atoms: 0.23 Number of scatterers: 7746 At special positions: 0 Unit cell: (98.463, 127.003, 115.587, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 30 16.00 P 2 15.00 O 1395 8.00 N 1313 7.00 C 5004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 325.9 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 501 " pdb="ZN ZN 2 501 " - pdb=" ND1 HIS 2 381 " pdb="ZN ZN 2 501 " - pdb=" SG CYS 2 379 " pdb="ZN ZN 2 501 " - pdb=" SG CYS 2 404 " pdb="ZN ZN 2 501 " - pdb=" SG CYS 2 401 " pdb=" ZN 9 601 " pdb="ZN ZN 9 601 " - pdb=" NE2 HIS 2 356 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 437 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 434 " pdb="ZN ZN 9 601 " - pdb=" SG CYS 9 395 " Number of angles added : 6 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 61.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain '2' and resid 2 through 13 removed outlier: 3.668A pdb=" N ALA 2 13 " --> pdb=" O GLU 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 55 Processing helix chain '2' and resid 70 through 111 removed outlier: 3.707A pdb=" N ILE 2 77 " --> pdb=" O LYS 2 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER 2 82 " --> pdb=" O ILE 2 78 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN 2 85 " --> pdb=" O LEU 2 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG 2 86 " --> pdb=" O SER 2 82 " (cutoff:3.500A) Processing helix chain '2' and resid 112 through 114 No H-bonds generated for 'chain '2' and resid 112 through 114' Processing helix chain '2' and resid 118 through 123 Processing helix chain '2' and resid 128 through 130 No H-bonds generated for 'chain '2' and resid 128 through 130' Processing helix chain '2' and resid 131 through 146 removed outlier: 3.547A pdb=" N VAL 2 135 " --> pdb=" O THR 2 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU 2 137 " --> pdb=" O GLU 2 133 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 2 140 " --> pdb=" O ASN 2 136 " (cutoff:3.500A) Processing helix chain '2' and resid 158 through 166 Processing helix chain '2' and resid 174 through 188 Processing helix chain '2' and resid 192 through 204 removed outlier: 3.794A pdb=" N GLU 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) Processing helix chain '2' and resid 209 through 226 Processing helix chain '2' and resid 280 through 300 Processing helix chain '2' and resid 306 through 332 removed outlier: 3.569A pdb=" N LEU 2 310 " --> pdb=" O SER 2 306 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE 2 317 " --> pdb=" O LEU 2 313 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS 2 324 " --> pdb=" O GLN 2 320 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 2 327 " --> pdb=" O ILE 2 323 " (cutoff:3.500A) Processing helix chain '2' and resid 349 through 353 removed outlier: 3.686A pdb=" N THR 2 353 " --> pdb=" O ASP 2 350 " (cutoff:3.500A) Processing helix chain '2' and resid 385 through 392 Processing helix chain '9' and resid 11 through 19 removed outlier: 3.543A pdb=" N ASN 9 19 " --> pdb=" O HIS 9 15 " (cutoff:3.500A) Processing helix chain '9' and resid 20 through 59 Proline residue: 9 26 - end of helix Processing helix chain '9' and resid 63 through 116 removed outlier: 3.819A pdb=" N GLN 9 97 " --> pdb=" O LYS 9 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE 9 98 " --> pdb=" O SER 9 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE 9 102 " --> pdb=" O ILE 9 98 " (cutoff:3.500A) Processing helix chain '9' and resid 129 through 154 removed outlier: 3.675A pdb=" N THR 9 133 " --> pdb=" O GLU 9 129 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS 9 134 " --> pdb=" O GLY 9 130 " (cutoff:3.500A) Processing helix chain '9' and resid 168 through 177 Processing helix chain '9' and resid 179 through 183 removed outlier: 3.686A pdb=" N ILE 9 183 " --> pdb=" O ASP 9 180 " (cutoff:3.500A) Processing helix chain '9' and resid 186 through 200 Processing helix chain '9' and resid 204 through 214 Processing helix chain '9' and resid 214 through 222 removed outlier: 3.541A pdb=" N LEU 9 218 " --> pdb=" O ASN 9 214 " (cutoff:3.500A) Processing helix chain '9' and resid 225 through 240 removed outlier: 4.175A pdb=" N VAL 9 240 " --> pdb=" O GLU 9 236 " (cutoff:3.500A) Processing helix chain '9' and resid 242 through 254 Processing helix chain '9' and resid 255 through 258 Processing helix chain '9' and resid 262 through 271 Processing helix chain '9' and resid 347 through 352 Processing helix chain '9' and resid 353 through 372 removed outlier: 4.109A pdb=" N SER 9 357 " --> pdb=" O ASP 9 353 " (cutoff:3.500A) Processing helix chain '9' and resid 377 through 390 removed outlier: 3.655A pdb=" N SER 9 388 " --> pdb=" O SER 9 384 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU 9 390 " --> pdb=" O GLY 9 386 " (cutoff:3.500A) Processing helix chain '9' and resid 422 through 429 removed outlier: 3.763A pdb=" N LEU 9 429 " --> pdb=" O THR 9 425 " (cutoff:3.500A) Processing helix chain '9' and resid 441 through 448 Processing helix chain '9' and resid 473 through 486 Processing helix chain '9' and resid 508 through 510 No H-bonds generated for 'chain '9' and resid 508 through 510' Processing helix chain 'E' and resid 5 through 18 removed outlier: 3.758A pdb=" N SER E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 98 through 112 Proline residue: E 108 - end of helix Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 133 through 147 removed outlier: 4.185A pdb=" N GLU E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 37 through 41 Processing helix chain 'U' and resid 55 through 59 removed outlier: 3.539A pdb=" N ASP U 58 " --> pdb=" O THR U 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 375 through 376 Processing sheet with id=AA2, first strand: chain '2' and resid 399 through 400 Processing sheet with id=AA3, first strand: chain '2' and resid 417 through 418 removed outlier: 6.585A pdb=" N ARG 2 417 " --> pdb=" O VAL 9 470 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ASP 9 472 " --> pdb=" O ARG 2 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9' and resid 495 through 498 removed outlier: 4.075A pdb=" N LYS 9 503 " --> pdb=" O ASP 9 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'U' and resid 12 through 16 removed outlier: 8.988A pdb=" N LEU U 67 " --> pdb=" O GLN U 2 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE U 4 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU U 69 " --> pdb=" O PHE U 4 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS U 6 " --> pdb=" O LEU U 69 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1293 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: 1.17 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1578 1.33 - 1.45: 1753 1.45 - 1.57: 4527 1.57 - 1.69: 2 1.69 - 1.81: 48 Bond restraints: 7908 Sorted by residual: bond pdb=" O1P SEP E 202 " pdb=" P SEP E 202 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O3P SEP E 202 " pdb=" P SEP E 202 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1P SEP E 207 " pdb=" P SEP E 207 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O2P SEP E 202 " pdb=" P SEP E 202 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O3P SEP E 207 " pdb=" P SEP E 207 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 7903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10440 2.10 - 4.20: 261 4.20 - 6.30: 37 6.30 - 8.40: 4 8.40 - 10.50: 2 Bond angle restraints: 10744 Sorted by residual: angle pdb=" N LEU E 120 " pdb=" CA LEU E 120 " pdb=" C LEU E 120 " ideal model delta sigma weight residual 113.50 107.54 5.96 1.23e+00 6.61e-01 2.35e+01 angle pdb=" N ILE 2 148 " pdb=" CA ILE 2 148 " pdb=" C ILE 2 148 " ideal model delta sigma weight residual 113.53 109.15 4.38 9.80e-01 1.04e+00 1.99e+01 angle pdb=" CA ASN 2 48 " pdb=" C ASN 2 48 " pdb=" O ASN 2 48 " ideal model delta sigma weight residual 120.70 116.37 4.33 1.03e+00 9.43e-01 1.77e+01 angle pdb=" N ASP E 200 " pdb=" CA ASP E 200 " pdb=" C ASP E 200 " ideal model delta sigma weight residual 112.47 107.35 5.12 1.24e+00 6.50e-01 1.70e+01 angle pdb=" CA ASP E 205 " pdb=" C ASP E 205 " pdb=" O ASP E 205 " ideal model delta sigma weight residual 121.87 117.65 4.22 1.10e+00 8.26e-01 1.47e+01 ... (remaining 10739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4232 16.94 - 33.88: 409 33.88 - 50.82: 89 50.82 - 67.76: 19 67.76 - 84.70: 5 Dihedral angle restraints: 4754 sinusoidal: 1762 harmonic: 2992 Sorted by residual: dihedral pdb=" CA HIS 2 380 " pdb=" C HIS 2 380 " pdb=" N HIS 2 381 " pdb=" CA HIS 2 381 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE 9 459 " pdb=" C PHE 9 459 " pdb=" N GLU 9 460 " pdb=" CA GLU 9 460 " ideal model delta harmonic sigma weight residual 180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA TRP E 105 " pdb=" C TRP E 105 " pdb=" N MET E 106 " pdb=" CA MET E 106 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 ... (remaining 4751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1034 0.056 - 0.113: 196 0.113 - 0.169: 25 0.169 - 0.226: 8 0.226 - 0.282: 2 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA SEP E 202 " pdb=" N SEP E 202 " pdb=" C SEP E 202 " pdb=" CB SEP E 202 " both_signs ideal model delta sigma weight residual False 2.50 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE E 204 " pdb=" N ILE E 204 " pdb=" C ILE E 204 " pdb=" CB ILE E 204 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE 2 51 " pdb=" N ILE 2 51 " pdb=" C ILE 2 51 " pdb=" CB ILE 2 51 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1262 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 138 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C LYS E 138 " 0.059 2.00e-02 2.50e+03 pdb=" O LYS E 138 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE E 139 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 141 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C GLU E 141 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU E 141 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR E 142 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 199 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C GLU E 199 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU E 199 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP E 200 " 0.014 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1827 2.79 - 3.32: 7480 3.32 - 3.85: 12074 3.85 - 4.37: 13437 4.37 - 4.90: 23899 Nonbonded interactions: 58717 Sorted by model distance: nonbonded pdb=" O PRO 2 362 " pdb=" NZ LYS 2 365 " model vdw 2.266 3.120 nonbonded pdb=" O GLU 9 162 " pdb=" OG1 THR 9 163 " model vdw 2.316 3.040 nonbonded pdb=" NZ LYS 9 215 " pdb=" OE2 GLU 9 226 " model vdw 2.341 3.120 nonbonded pdb=" OE2 GLU 2 341 " pdb=" ND1 HIS 9 452 " model vdw 2.342 3.120 nonbonded pdb=" O SER 9 117 " pdb=" OG SER 9 117 " model vdw 2.376 3.040 ... (remaining 58712 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.005 0.096 7917 Z= 0.313 Angle : 0.748 10.504 10750 Z= 0.449 Chirality : 0.048 0.282 1265 Planarity : 0.005 0.092 1346 Dihedral : 14.379 84.696 2794 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.50 % Allowed : 1.01 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.28), residues: 981 helix: 1.77 (0.23), residues: 561 sheet: 0.23 (0.86), residues: 41 loop : -1.68 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 6 TYR 0.018 0.002 TYR 9 95 PHE 0.013 0.001 PHE 9 87 TRP 0.007 0.001 TRP E 105 HIS 0.003 0.001 HIS 2 356 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 7908) covalent geometry : angle 0.73593 (10744) hydrogen bonds : bond 0.13545 ( 445) hydrogen bonds : angle 5.12558 ( 1293) metal coordination : bond 0.02435 ( 8) metal coordination : angle 5.66101 ( 6) Misc. bond : bond 0.06842 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.267 Fit side-chains REVERT: 2 49 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7999 (ttmm) REVERT: 2 329 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7502 (tpp-160) outliers start: 4 outliers final: 0 residues processed: 136 average time/residue: 0.0857 time to fit residues: 15.6860 Evaluate side-chains 108 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 52 GLN 2 320 GLN U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113386 restraints weight = 11570.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114290 restraints weight = 7443.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115196 restraints weight = 5560.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115523 restraints weight = 5086.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115675 restraints weight = 4329.242| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7917 Z= 0.140 Angle : 0.556 10.726 10750 Z= 0.279 Chirality : 0.040 0.153 1265 Planarity : 0.004 0.047 1346 Dihedral : 4.873 54.546 1070 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.51 % Allowed : 8.69 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.28), residues: 981 helix: 2.32 (0.22), residues: 567 sheet: 0.37 (0.86), residues: 39 loop : -1.56 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 6 TYR 0.019 0.002 TYR 9 95 PHE 0.012 0.001 PHE 9 7 TRP 0.006 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7908) covalent geometry : angle 0.54895 (10744) hydrogen bonds : bond 0.05275 ( 445) hydrogen bonds : angle 3.98474 ( 1293) metal coordination : bond 0.00781 ( 8) metal coordination : angle 3.73705 ( 6) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.323 Fit side-chains REVERT: 2 49 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7801 (tmtt) REVERT: 2 226 MET cc_start: 0.4310 (ttm) cc_final: 0.3890 (ttm) REVERT: 2 324 LYS cc_start: 0.8466 (tttt) cc_final: 0.8220 (tttp) REVERT: 9 234 TYR cc_start: 0.7855 (t80) cc_final: 0.7153 (t80) REVERT: 9 370 MET cc_start: 0.8701 (ttt) cc_final: 0.8495 (ttt) REVERT: E 135 TYR cc_start: 0.6748 (t80) cc_final: 0.6387 (t80) outliers start: 12 outliers final: 9 residues processed: 122 average time/residue: 0.0806 time to fit residues: 13.3855 Evaluate side-chains 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111111 restraints weight = 11463.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112518 restraints weight = 7227.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112985 restraints weight = 5455.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113243 restraints weight = 5198.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113421 restraints weight = 4516.976| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7917 Z= 0.149 Angle : 0.556 10.418 10750 Z= 0.281 Chirality : 0.040 0.141 1265 Planarity : 0.004 0.045 1346 Dihedral : 4.636 56.717 1070 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.39 % Allowed : 11.08 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.28), residues: 981 helix: 2.48 (0.22), residues: 566 sheet: 0.31 (0.87), residues: 39 loop : -1.52 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 105 TYR 0.020 0.002 TYR 9 95 PHE 0.013 0.001 PHE 9 7 TRP 0.006 0.001 TRP E 93 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7908) covalent geometry : angle 0.54767 (10744) hydrogen bonds : bond 0.05222 ( 445) hydrogen bonds : angle 3.87894 ( 1293) metal coordination : bond 0.01044 ( 8) metal coordination : angle 3.97462 ( 6) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.202 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8499 (m-80) cc_final: 0.8117 (t80) REVERT: 2 226 MET cc_start: 0.4323 (ttm) cc_final: 0.3830 (ttm) REVERT: 2 324 LYS cc_start: 0.8417 (tttt) cc_final: 0.8198 (tttp) REVERT: 9 234 TYR cc_start: 0.7912 (t80) cc_final: 0.7307 (t80) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 0.0807 time to fit residues: 13.3187 Evaluate side-chains 115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108891 restraints weight = 11894.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110930 restraints weight = 7138.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112375 restraints weight = 5121.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113160 restraints weight = 4108.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113846 restraints weight = 3586.846| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7917 Z= 0.162 Angle : 0.568 9.974 10750 Z= 0.286 Chirality : 0.040 0.150 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.248 31.044 1066 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.27 % Allowed : 12.72 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.28), residues: 981 helix: 2.53 (0.22), residues: 562 sheet: 0.15 (0.86), residues: 39 loop : -1.52 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 105 TYR 0.020 0.002 TYR 9 95 PHE 0.014 0.001 PHE 9 7 TRP 0.007 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 83 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7908) covalent geometry : angle 0.55789 (10744) hydrogen bonds : bond 0.05327 ( 445) hydrogen bonds : angle 3.90486 ( 1293) metal coordination : bond 0.01194 ( 8) metal coordination : angle 4.47851 ( 6) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.301 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8621 (m-80) cc_final: 0.8210 (t80) REVERT: 2 324 LYS cc_start: 0.8396 (tttt) cc_final: 0.8167 (tttp) REVERT: 9 224 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8503 (pp) REVERT: 9 234 TYR cc_start: 0.8034 (t80) cc_final: 0.7427 (t80) REVERT: 9 497 MET cc_start: 0.8004 (ttp) cc_final: 0.7398 (ttt) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.0855 time to fit residues: 14.0745 Evaluate side-chains 122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN E 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110599 restraints weight = 11624.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111450 restraints weight = 7448.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112710 restraints weight = 5691.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112925 restraints weight = 5048.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113069 restraints weight = 4279.091| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7917 Z= 0.150 Angle : 0.553 9.825 10750 Z= 0.279 Chirality : 0.040 0.141 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.204 30.353 1066 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.27 % Allowed : 13.60 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.28), residues: 981 helix: 2.47 (0.22), residues: 567 sheet: 0.09 (0.86), residues: 39 loop : -1.52 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 105 TYR 0.020 0.002 TYR 9 95 PHE 0.013 0.001 PHE 9 7 TRP 0.011 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 83 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7908) covalent geometry : angle 0.54457 (10744) hydrogen bonds : bond 0.05153 ( 445) hydrogen bonds : angle 3.85489 ( 1293) metal coordination : bond 0.01092 ( 8) metal coordination : angle 3.99944 ( 6) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.261 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8582 (m-80) cc_final: 0.8216 (t80) REVERT: 2 324 LYS cc_start: 0.8337 (tttt) cc_final: 0.8093 (tttp) REVERT: 9 224 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8510 (pp) REVERT: 9 234 TYR cc_start: 0.8102 (t80) cc_final: 0.7415 (t80) REVERT: 9 497 MET cc_start: 0.8009 (ttp) cc_final: 0.7472 (ttt) REVERT: U 31 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8456 (tm-30) outliers start: 26 outliers final: 20 residues processed: 126 average time/residue: 0.0768 time to fit residues: 13.5960 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 84 ILE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 0.0030 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN E 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111860 restraints weight = 11573.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113873 restraints weight = 7113.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115030 restraints weight = 5149.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115982 restraints weight = 4196.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116566 restraints weight = 3648.218| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7917 Z= 0.123 Angle : 0.530 9.825 10750 Z= 0.267 Chirality : 0.039 0.157 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.048 29.468 1066 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.77 % Allowed : 14.61 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.28), residues: 981 helix: 2.54 (0.22), residues: 566 sheet: 0.07 (0.84), residues: 40 loop : -1.53 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 417 TYR 0.018 0.002 TYR 2 296 PHE 0.012 0.001 PHE 9 7 TRP 0.010 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 83 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7908) covalent geometry : angle 0.52397 (10744) hydrogen bonds : bond 0.04688 ( 445) hydrogen bonds : angle 3.73384 ( 1293) metal coordination : bond 0.00828 ( 8) metal coordination : angle 3.42570 ( 6) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.339 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8545 (m-80) cc_final: 0.8173 (t80) REVERT: 2 324 LYS cc_start: 0.8278 (tttt) cc_final: 0.8043 (tttp) REVERT: 9 224 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (pp) REVERT: 9 234 TYR cc_start: 0.8043 (t80) cc_final: 0.7371 (t80) REVERT: 9 497 MET cc_start: 0.8051 (ttp) cc_final: 0.7461 (ttt) REVERT: U 31 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8343 (tm-30) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 0.0829 time to fit residues: 14.3790 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112047 restraints weight = 11583.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112891 restraints weight = 7381.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114104 restraints weight = 5591.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114407 restraints weight = 5030.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114445 restraints weight = 4184.247| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7917 Z= 0.142 Angle : 0.550 10.293 10750 Z= 0.278 Chirality : 0.040 0.144 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.087 28.991 1066 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.77 % Allowed : 15.49 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.28), residues: 981 helix: 2.52 (0.22), residues: 567 sheet: -0.14 (0.83), residues: 41 loop : -1.53 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 417 TYR 0.019 0.002 TYR 9 95 PHE 0.013 0.001 PHE 9 7 TRP 0.012 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 83 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7908) covalent geometry : angle 0.54302 (10744) hydrogen bonds : bond 0.04939 ( 445) hydrogen bonds : angle 3.75731 ( 1293) metal coordination : bond 0.01080 ( 8) metal coordination : angle 3.81654 ( 6) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.321 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8579 (m-80) cc_final: 0.8193 (t80) REVERT: 2 324 LYS cc_start: 0.8159 (tttt) cc_final: 0.7895 (tttp) REVERT: 9 224 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8507 (pp) REVERT: 9 234 TYR cc_start: 0.8102 (t80) cc_final: 0.7414 (t80) REVERT: 9 265 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8418 (tt) REVERT: 9 497 MET cc_start: 0.8054 (ttp) cc_final: 0.7517 (ttt) REVERT: U 31 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8391 (tm-30) REVERT: U 40 GLN cc_start: 0.8388 (pt0) cc_final: 0.8181 (pt0) outliers start: 22 outliers final: 19 residues processed: 124 average time/residue: 0.0826 time to fit residues: 14.0387 Evaluate side-chains 129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 208 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109524 restraints weight = 11717.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111417 restraints weight = 7267.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112767 restraints weight = 5280.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113473 restraints weight = 4261.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114084 restraints weight = 3745.071| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7917 Z= 0.159 Angle : 0.568 9.973 10750 Z= 0.288 Chirality : 0.040 0.167 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.186 29.483 1066 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.90 % Allowed : 16.12 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.28), residues: 981 helix: 2.44 (0.22), residues: 568 sheet: -0.35 (0.83), residues: 42 loop : -1.53 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 105 TYR 0.020 0.002 TYR 9 95 PHE 0.014 0.001 PHE 9 7 TRP 0.012 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7908) covalent geometry : angle 0.55978 (10744) hydrogen bonds : bond 0.05223 ( 445) hydrogen bonds : angle 3.82910 ( 1293) metal coordination : bond 0.01299 ( 8) metal coordination : angle 4.16990 ( 6) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.304 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8608 (m-80) cc_final: 0.8189 (t80) REVERT: 2 324 LYS cc_start: 0.8202 (tttt) cc_final: 0.7947 (tttp) REVERT: 9 224 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8535 (pp) REVERT: 9 234 TYR cc_start: 0.8150 (t80) cc_final: 0.7469 (t80) REVERT: 9 265 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8430 (tt) REVERT: 9 497 MET cc_start: 0.8060 (ttp) cc_final: 0.7483 (ttt) REVERT: U 31 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8390 (tm-30) outliers start: 23 outliers final: 19 residues processed: 122 average time/residue: 0.0773 time to fit residues: 12.8738 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 320 GLN Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 84 ILE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 208 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN U 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108035 restraints weight = 11649.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109931 restraints weight = 7258.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111307 restraints weight = 5308.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112091 restraints weight = 4288.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112675 restraints weight = 3753.329| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7917 Z= 0.183 Angle : 0.601 11.625 10750 Z= 0.302 Chirality : 0.041 0.164 1265 Planarity : 0.004 0.043 1346 Dihedral : 4.289 29.632 1066 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.02 % Allowed : 16.25 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.28), residues: 981 helix: 2.40 (0.22), residues: 567 sheet: -0.38 (0.83), residues: 42 loop : -1.54 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 9 105 TYR 0.021 0.002 TYR 9 95 PHE 0.015 0.002 PHE 9 7 TRP 0.013 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7908) covalent geometry : angle 0.59118 (10744) hydrogen bonds : bond 0.05519 ( 445) hydrogen bonds : angle 3.92465 ( 1293) metal coordination : bond 0.01508 ( 8) metal coordination : angle 4.55881 ( 6) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.237 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8634 (m-80) cc_final: 0.8183 (t80) REVERT: 2 324 LYS cc_start: 0.8243 (tttt) cc_final: 0.7980 (tttp) REVERT: 9 224 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (pp) REVERT: 9 234 TYR cc_start: 0.8183 (t80) cc_final: 0.7508 (t80) REVERT: 9 265 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8426 (tt) REVERT: 9 497 MET cc_start: 0.8098 (ttp) cc_final: 0.7503 (ttt) REVERT: U 31 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8473 (tm-30) outliers start: 24 outliers final: 21 residues processed: 118 average time/residue: 0.0705 time to fit residues: 11.5435 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 320 GLN Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 84 ILE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 208 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 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 = 0.3512 r_free = 0.3512 target = 0.130418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111307 restraints weight = 11640.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113422 restraints weight = 7027.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114831 restraints weight = 5016.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115549 restraints weight = 4013.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116284 restraints weight = 3522.758| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7917 Z= 0.126 Angle : 0.541 9.904 10750 Z= 0.275 Chirality : 0.039 0.164 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.116 30.099 1066 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.64 % Allowed : 16.62 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.28), residues: 981 helix: 2.52 (0.22), residues: 567 sheet: -0.23 (0.83), residues: 41 loop : -1.49 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 6 TYR 0.018 0.002 TYR 9 159 PHE 0.012 0.001 PHE 9 7 TRP 0.015 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 83 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7908) covalent geometry : angle 0.53460 (10744) hydrogen bonds : bond 0.04764 ( 445) hydrogen bonds : angle 3.73470 ( 1293) metal coordination : bond 0.00972 ( 8) metal coordination : angle 3.60806 ( 6) Misc. bond : bond 0.00023 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.216 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8532 (m-80) cc_final: 0.8151 (t80) REVERT: 2 324 LYS cc_start: 0.8094 (tttt) cc_final: 0.7866 (tttp) REVERT: 9 224 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8521 (pp) REVERT: 9 234 TYR cc_start: 0.8088 (t80) cc_final: 0.7426 (t80) REVERT: 9 265 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8375 (tt) REVERT: 9 497 MET cc_start: 0.8063 (ttp) cc_final: 0.7507 (ttt) REVERT: E 106 MET cc_start: 0.7530 (ptp) cc_final: 0.7019 (ptp) REVERT: U 31 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8412 (tm-30) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.0722 time to fit residues: 11.5180 Evaluate side-chains 124 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 208 ILE Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.0030 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN ** E 101 ASN ** 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 = 0.3514 r_free = 0.3514 target = 0.130581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112082 restraints weight = 11599.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114092 restraints weight = 7157.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115448 restraints weight = 5157.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116171 restraints weight = 4128.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116888 restraints weight = 3628.154| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7917 Z= 0.126 Angle : 0.535 9.776 10750 Z= 0.271 Chirality : 0.039 0.157 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.029 28.516 1066 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.77 % Allowed : 16.37 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.28), residues: 981 helix: 2.50 (0.22), residues: 572 sheet: -0.18 (0.83), residues: 41 loop : -1.50 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 105 TYR 0.017 0.001 TYR 9 95 PHE 0.012 0.001 PHE 9 7 TRP 0.016 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 83 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7908) covalent geometry : angle 0.52875 (10744) hydrogen bonds : bond 0.04617 ( 445) hydrogen bonds : angle 3.68803 ( 1293) metal coordination : bond 0.00996 ( 8) metal coordination : angle 3.59782 ( 6) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.86 seconds wall clock time: 21 minutes 20.68 seconds (1280.68 seconds total)