Starting phenix.real_space_refine on Wed Feb 12 10:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pmq_17764/02_2025/8pmq_17764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmq_17764/02_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_17764/02_2025/8pmq_17764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmq_17764/02_2025/8pmq_17764.map" model { file = "/net/cci-nas-00/data/ceres_data/8pmq_17764/02_2025/8pmq_17764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmq_17764/02_2025/8pmq_17764.cif" } resolution = 3.53 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= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 14} 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: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 8} 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, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} 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: 4.75, per 1000 atoms: 0.61 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: 2.23 Conformation dependent library (CDL) restraints added in 984.1 milliseconds 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: 0.65 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: 1.75 Time building geometry restraints manager: 2.36 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- 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 7908 Z= 0.353 Angle : 0.736 10.504 10744 Z= 0.447 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 : 6.53 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 (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: 0.65 (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 TRP 0.007 0.001 TRP E 105 HIS 0.003 0.001 HIS 2 356 PHE 0.013 0.001 PHE 9 87 TYR 0.018 0.002 TYR 9 95 ARG 0.006 0.001 ARG E 6 *********************** 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 : 0.943 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: 0.2112 time to fit residues: 38.6342 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 : 0.944 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 52 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 = 0.3471 r_free = 0.3471 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108887 restraints weight = 11372.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110652 restraints weight = 7078.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111909 restraints weight = 5198.068| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7908 Z= 0.285 Angle : 0.585 10.684 10744 Z= 0.298 Chirality : 0.041 0.160 1265 Planarity : 0.004 0.047 1346 Dihedral : 4.957 55.591 1070 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.76 % Allowed : 8.94 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 981 helix: 2.24 (0.22), residues: 565 sheet: 0.30 (0.87), residues: 39 loop : -1.65 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 105 HIS 0.003 0.001 HIS 9 51 PHE 0.014 0.001 PHE 9 7 TYR 0.021 0.002 TYR 9 95 ARG 0.004 0.001 ARG E 6 *********************** 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: 14 poor density : 114 time to evaluate : 0.890 Fit side-chains REVERT: 2 49 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7795 (tmtt) REVERT: 2 226 MET cc_start: 0.4084 (ttm) cc_final: 0.3753 (ttm) REVERT: 9 234 TYR cc_start: 0.8071 (t80) cc_final: 0.7492 (t80) REVERT: E 135 TYR cc_start: 0.6663 (t80) cc_final: 0.6455 (t80) REVERT: U 33 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (ttmt) outliers start: 14 outliers final: 11 residues processed: 122 average time/residue: 0.2065 time to fit residues: 34.0701 Evaluate side-chains 117 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 84 ILE 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 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.129399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111892 restraints weight = 11665.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112784 restraints weight = 7501.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114081 restraints weight = 5715.495| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7908 Z= 0.234 Angle : 0.546 10.334 10744 Z= 0.279 Chirality : 0.040 0.144 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.672 56.880 1070 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.27 % Allowed : 11.71 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 981 helix: 2.44 (0.22), residues: 566 sheet: 0.22 (0.87), residues: 39 loop : -1.60 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.013 0.001 PHE 9 7 TYR 0.019 0.002 TYR 9 95 ARG 0.003 0.000 ARG 9 105 *********************** 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 129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.866 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8501 (m-80) cc_final: 0.8082 (t80) REVERT: 2 324 LYS cc_start: 0.8395 (tttt) cc_final: 0.8150 (tttp) REVERT: 9 234 TYR cc_start: 0.8086 (t80) cc_final: 0.7317 (t80) REVERT: 9 238 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6536 (tp) REVERT: 9 497 MET cc_start: 0.7901 (ttp) cc_final: 0.7453 (ttt) REVERT: E 135 TYR cc_start: 0.6945 (t80) cc_final: 0.6737 (t80) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 0.2022 time to fit residues: 33.3082 Evaluate side-chains 116 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN 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 238 LEU Chi-restraints excluded: chain 9 residue 351 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 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 = 0.3475 r_free = 0.3475 target = 0.127504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108867 restraints weight = 11595.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110811 restraints weight = 7165.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111984 restraints weight = 5211.263| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7908 Z= 0.258 Angle : 0.560 10.009 10744 Z= 0.286 Chirality : 0.040 0.151 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.285 30.734 1066 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.64 % Allowed : 12.97 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.28), residues: 981 helix: 2.50 (0.22), residues: 562 sheet: 0.11 (0.86), residues: 39 loop : -1.62 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.014 0.001 PHE 9 7 TYR 0.020 0.002 TYR 9 95 ARG 0.004 0.000 ARG 9 105 *********************** 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 134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.816 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8615 (m-80) cc_final: 0.8235 (t80) REVERT: 2 324 LYS cc_start: 0.8375 (tttt) cc_final: 0.8108 (tttp) REVERT: 9 224 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8521 (pp) REVERT: 9 234 TYR cc_start: 0.8106 (t80) cc_final: 0.7331 (t80) REVERT: 9 238 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6740 (tp) REVERT: 9 497 MET cc_start: 0.8004 (ttp) cc_final: 0.7386 (ttt) REVERT: E 135 TYR cc_start: 0.6876 (t80) cc_final: 0.6644 (t80) outliers start: 21 outliers final: 16 residues processed: 124 average time/residue: 0.1969 time to fit residues: 33.3754 Evaluate side-chains 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 0.0010 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109554 restraints weight = 11492.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111498 restraints weight = 7113.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112722 restraints weight = 5176.313| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7908 Z= 0.240 Angle : 0.545 9.812 10744 Z= 0.279 Chirality : 0.040 0.149 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.236 30.312 1066 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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 (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: 1.34 (0.28), residues: 981 helix: 2.45 (0.22), residues: 568 sheet: 0.10 (0.86), residues: 39 loop : -1.61 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.013 0.001 PHE 9 7 TYR 0.019 0.001 TYR 9 95 ARG 0.002 0.000 ARG 9 105 *********************** 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 134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.894 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8584 (m-80) cc_final: 0.8193 (t80) REVERT: 2 324 LYS cc_start: 0.8347 (tttt) cc_final: 0.8106 (tttp) REVERT: 9 234 TYR cc_start: 0.8085 (t80) cc_final: 0.7316 (t80) REVERT: 9 238 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6720 (tp) REVERT: 9 497 MET cc_start: 0.8074 (ttp) cc_final: 0.7491 (ttt) REVERT: E 135 TYR cc_start: 0.6859 (t80) cc_final: 0.6626 (t80) REVERT: U 31 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 0.2020 time to fit residues: 34.0475 Evaluate side-chains 122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 96 CYS Chi-restraints excluded: chain 9 residue 145 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 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 10 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.126308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107697 restraints weight = 11568.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109555 restraints weight = 7233.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110859 restraints weight = 5325.671| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7908 Z= 0.301 Angle : 0.587 9.651 10744 Z= 0.299 Chirality : 0.041 0.160 1265 Planarity : 0.004 0.043 1346 Dihedral : 4.338 30.045 1066 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.90 % Allowed : 15.11 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 981 helix: 2.36 (0.22), residues: 566 sheet: -0.35 (0.83), residues: 42 loop : -1.62 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.015 0.001 PHE 9 7 TYR 0.021 0.002 TYR 9 95 ARG 0.003 0.000 ARG 9 105 *********************** 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 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.030 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8632 (m-80) cc_final: 0.8198 (t80) REVERT: 2 324 LYS cc_start: 0.8386 (tttt) cc_final: 0.8121 (tttp) REVERT: 9 234 TYR cc_start: 0.8132 (t80) cc_final: 0.7411 (t80) REVERT: 9 238 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6746 (tp) REVERT: 9 497 MET cc_start: 0.8119 (ttp) cc_final: 0.7523 (ttt) REVERT: E 135 TYR cc_start: 0.6872 (t80) cc_final: 0.6629 (t80) REVERT: U 31 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8400 (tm-30) outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 0.2006 time to fit residues: 32.9566 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 238 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 Chi-restraints excluded: chain U residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 85 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.127472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108827 restraints weight = 11607.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110819 restraints weight = 7211.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112098 restraints weight = 5239.010| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7908 Z= 0.236 Angle : 0.553 10.225 10744 Z= 0.283 Chirality : 0.040 0.142 1265 Planarity : 0.004 0.043 1346 Dihedral : 4.221 30.414 1066 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.90 % Allowed : 15.87 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 981 helix: 2.43 (0.22), residues: 567 sheet: -0.33 (0.83), residues: 42 loop : -1.64 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.013 0.001 PHE 9 7 TYR 0.019 0.002 TYR 9 95 ARG 0.007 0.000 ARG 2 417 *********************** 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 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.928 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8598 (m-80) cc_final: 0.8191 (t80) REVERT: 2 324 LYS cc_start: 0.8312 (tttt) cc_final: 0.8063 (tttp) REVERT: 9 234 TYR cc_start: 0.8092 (t80) cc_final: 0.7389 (t80) REVERT: 9 238 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6686 (tp) REVERT: 9 265 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8462 (tt) REVERT: 9 347 TYR cc_start: 0.8172 (m-80) cc_final: 0.7959 (m-80) REVERT: 9 497 MET cc_start: 0.8116 (ttp) cc_final: 0.7542 (ttt) REVERT: U 31 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8366 (tm-30) outliers start: 23 outliers final: 18 residues processed: 120 average time/residue: 0.2024 time to fit residues: 33.3222 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain U residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 0.0050 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.128496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109858 restraints weight = 11625.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111824 restraints weight = 7161.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112944 restraints weight = 5186.012| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7908 Z= 0.209 Angle : 0.537 9.568 10744 Z= 0.277 Chirality : 0.039 0.161 1265 Planarity : 0.004 0.045 1346 Dihedral : 4.138 29.653 1066 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.52 % Allowed : 17.00 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 981 helix: 2.47 (0.22), residues: 568 sheet: -0.20 (0.83), residues: 41 loop : -1.55 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.012 0.001 PHE 9 7 TYR 0.018 0.002 TYR 9 95 ARG 0.002 0.000 ARG 9 105 *********************** 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 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.954 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8552 (m-80) cc_final: 0.8175 (t80) REVERT: 2 324 LYS cc_start: 0.8150 (tttt) cc_final: 0.7895 (tttp) REVERT: 9 234 TYR cc_start: 0.8091 (t80) cc_final: 0.7339 (t80) REVERT: 9 265 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8466 (tt) REVERT: 9 347 TYR cc_start: 0.8057 (m-80) cc_final: 0.7762 (m-80) REVERT: 9 497 MET cc_start: 0.8048 (ttp) cc_final: 0.7442 (ttt) REVERT: U 31 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8379 (tm-30) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 0.2037 time to fit residues: 34.3670 Evaluate side-chains 122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 48 LEU Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE 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 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110094 restraints weight = 11807.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111137 restraints weight = 7631.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111823 restraints weight = 5655.382| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7908 Z= 0.262 Angle : 0.580 11.650 10744 Z= 0.295 Chirality : 0.041 0.171 1265 Planarity : 0.004 0.043 1346 Dihedral : 4.227 29.362 1066 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.02 % Allowed : 16.50 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 981 helix: 2.44 (0.22), residues: 566 sheet: -0.42 (0.82), residues: 42 loop : -1.56 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.014 0.001 PHE 9 7 TYR 0.020 0.002 TYR 9 95 ARG 0.002 0.000 ARG 9 105 *********************** 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 133 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.866 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8615 (m-80) cc_final: 0.8191 (t80) REVERT: 2 324 LYS cc_start: 0.8197 (tttt) cc_final: 0.7942 (tttp) REVERT: 9 265 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8497 (tt) REVERT: 9 347 TYR cc_start: 0.8092 (m-80) cc_final: 0.7731 (m-80) REVERT: 9 497 MET cc_start: 0.8096 (ttp) cc_final: 0.7487 (ttt) REVERT: U 31 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8399 (tm-30) outliers start: 24 outliers final: 20 residues processed: 124 average time/residue: 0.1985 time to fit residues: 33.8623 Evaluate side-chains 126 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 48 LEU 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 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 425 THR 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 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 11 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3495 r_free = 0.3495 target = 0.129102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110461 restraints weight = 11711.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112432 restraints weight = 7162.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113611 restraints weight = 5169.157| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7908 Z= 0.204 Angle : 0.547 10.057 10744 Z= 0.280 Chirality : 0.040 0.173 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.091 29.377 1066 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.52 % Allowed : 17.00 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 981 helix: 2.54 (0.22), residues: 566 sheet: -0.27 (0.83), residues: 41 loop : -1.52 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.012 0.001 PHE 9 7 TYR 0.017 0.002 TYR 9 95 ARG 0.002 0.000 ARG E 6 ********************** 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 131 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.955 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8539 (m-80) cc_final: 0.8175 (t80) REVERT: 2 324 LYS cc_start: 0.8167 (tttt) cc_final: 0.7929 (tttp) REVERT: 9 234 TYR cc_start: 0.8077 (t80) cc_final: 0.7291 (t80) REVERT: 9 238 LEU cc_start: 0.7741 (tp) cc_final: 0.7364 (mt) REVERT: 9 265 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8391 (tt) REVERT: 9 347 TYR cc_start: 0.8106 (m-80) cc_final: 0.7770 (m-80) REVERT: 9 497 MET cc_start: 0.8042 (ttp) cc_final: 0.7429 (ttt) REVERT: U 31 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8436 (tm-30) outliers start: 20 outliers final: 19 residues processed: 123 average time/residue: 0.1981 time to fit residues: 33.5052 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 48 LEU 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 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 425 THR 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 61 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 84 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 46 HIS 2 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113502 restraints weight = 11580.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115319 restraints weight = 7168.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116703 restraints weight = 5241.065| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7908 Z= 0.195 Angle : 0.540 9.569 10744 Z= 0.276 Chirality : 0.039 0.170 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.019 28.107 1066 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.77 % Allowed : 16.75 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 981 helix: 2.51 (0.22), residues: 572 sheet: -0.26 (0.83), residues: 41 loop : -1.50 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.012 0.001 PHE 9 7 TYR 0.016 0.001 TYR 9 95 ARG 0.002 0.000 ARG E 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.12 seconds wall clock time: 42 minutes 1.38 seconds (2521.38 seconds total)