Starting phenix.real_space_refine on Sun May 11 08:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pmq_17764/05_2025/8pmq_17764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmq_17764/05_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_17764/05_2025/8pmq_17764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmq_17764/05_2025/8pmq_17764.map" model { file = "/net/cci-nas-00/data/ceres_data/8pmq_17764/05_2025/8pmq_17764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmq_17764/05_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-5687/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: 4.73, 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: 1.95 Conformation dependent library (CDL) restraints added in 997.4 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: 0.79 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: 2.07 Time building geometry restraints manager: 2.26 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: 0.880 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.880 Find NCS groups from input model: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- 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 : 6.53 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 Details of bonding type rmsd hydrogen bonds : bond 0.13545 ( 445) hydrogen bonds : angle 5.12558 ( 1293) metal coordination : bond 0.02435 ( 8) metal coordination : angle 5.66101 ( 6) covalent geometry : bond 0.00534 ( 7908) covalent geometry : angle 0.73593 (10744) 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 : 0.880 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: 0.2065 time to fit residues: 37.4037 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 : 0.876 ------------------------------------------------------------------------------- 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 7917 Z= 0.179 Angle : 0.594 10.684 10750 Z= 0.299 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 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 445) hydrogen bonds : angle 4.11950 ( 1293) metal coordination : bond 0.00973 ( 8) metal coordination : angle 4.38280 ( 6) covalent geometry : bond 0.00434 ( 7908) covalent geometry : angle 0.58522 (10744) Misc. bond : bond 0.00043 ( 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: 14 poor density : 114 time to evaluate : 0.995 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: 0.2056 time to fit residues: 34.0559 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 : 0.967 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9990 chunk 59 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111486 restraints weight = 11666.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112430 restraints weight = 7504.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113510 restraints weight = 5693.779| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7917 Z= 0.155 Angle : 0.560 10.316 10750 Z= 0.283 Chirality : 0.040 0.145 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.700 57.123 1070 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.39 % Allowed : 11.59 % 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: 1.31 (0.28), residues: 981 helix: 2.42 (0.22), residues: 566 sheet: 0.21 (0.87), residues: 39 loop : -1.61 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 93 HIS 0.003 0.001 HIS E 33 PHE 0.013 0.001 PHE 9 7 TYR 0.020 0.002 TYR 9 95 ARG 0.004 0.000 ARG 9 105 Details of bonding type rmsd hydrogen bonds : bond 0.05358 ( 445) hydrogen bonds : angle 3.94720 ( 1293) metal coordination : bond 0.01040 ( 8) metal coordination : angle 4.08129 ( 6) covalent geometry : bond 0.00371 ( 7908) covalent geometry : angle 0.55196 (10744) Misc. bond : bond 0.00040 ( 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 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.892 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8518 (m-80) cc_final: 0.8092 (t80) REVERT: 2 324 LYS cc_start: 0.8402 (tttt) cc_final: 0.8140 (tttp) REVERT: 9 234 TYR cc_start: 0.8095 (t80) cc_final: 0.7325 (t80) REVERT: 9 238 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6508 (tp) REVERT: 9 497 MET cc_start: 0.7915 (ttp) cc_final: 0.7462 (ttt) REVERT: E 135 TYR cc_start: 0.6950 (t80) cc_final: 0.6744 (t80) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 0.1889 time to fit residues: 31.8574 Evaluate side-chains 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 6 optimal weight: 0.6980 chunk 59 optimal weight: 0.0020 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.129360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110824 restraints weight = 11607.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112755 restraints weight = 7209.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113888 restraints weight = 5280.775| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7917 Z= 0.149 Angle : 0.560 10.055 10750 Z= 0.283 Chirality : 0.040 0.144 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.233 30.790 1066 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.52 % Allowed : 13.35 % Favored : 84.13 % 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: 1.37 (0.28), residues: 981 helix: 2.50 (0.22), residues: 564 sheet: 0.08 (0.86), residues: 39 loop : -1.61 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 445) hydrogen bonds : angle 3.89372 ( 1293) metal coordination : bond 0.01080 ( 8) metal coordination : angle 4.30276 ( 6) covalent geometry : bond 0.00356 ( 7908) covalent geometry : angle 0.55131 (10744) Misc. bond : bond 0.00044 ( 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: 20 poor density : 110 time to evaluate : 1.009 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8581 (m-80) cc_final: 0.8222 (t80) REVERT: 2 324 LYS cc_start: 0.8371 (tttt) cc_final: 0.8124 (tttp) REVERT: 9 224 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8515 (pp) REVERT: 9 234 TYR cc_start: 0.8086 (t80) cc_final: 0.7322 (t80) REVERT: 9 238 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6727 (tp) REVERT: 9 497 MET cc_start: 0.7988 (ttp) cc_final: 0.7370 (ttt) REVERT: E 135 TYR cc_start: 0.6857 (t80) cc_final: 0.6634 (t80) outliers start: 20 outliers final: 16 residues processed: 120 average time/residue: 0.2063 time to fit residues: 33.8086 Evaluate side-chains 124 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 76 LEU 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 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: 0.2980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 11 optimal weight: 0.0040 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.130132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111617 restraints weight = 11431.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113612 restraints weight = 7024.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114843 restraints weight = 5054.905| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1444 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= 0.124 Angle : 0.526 9.903 10750 Z= 0.266 Chirality : 0.039 0.143 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.087 29.686 1066 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.64 % Allowed : 14.74 % 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: 1.51 (0.28), residues: 981 helix: 2.62 (0.22), residues: 562 sheet: 0.33 (0.86), residues: 38 loop : -1.56 (0.31), residues: 381 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 0.012 0.001 PHE 9 7 TYR 0.017 0.001 TYR 9 95 ARG 0.002 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 445) hydrogen bonds : angle 3.74190 ( 1293) metal coordination : bond 0.00855 ( 8) metal coordination : angle 3.52866 ( 6) covalent geometry : bond 0.00287 ( 7908) covalent geometry : angle 0.51970 (10744) Misc. bond : bond 0.00032 ( 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 138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.908 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8526 (m-80) cc_final: 0.8175 (t80) REVERT: 2 324 LYS cc_start: 0.8301 (tttt) cc_final: 0.8067 (tttp) REVERT: 9 224 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8522 (pp) REVERT: 9 234 TYR cc_start: 0.8035 (t80) cc_final: 0.7272 (t80) REVERT: 9 238 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6672 (tp) REVERT: 9 497 MET cc_start: 0.8033 (ttp) cc_final: 0.7369 (ttt) REVERT: E 135 TYR cc_start: 0.6904 (t80) cc_final: 0.6685 (t80) REVERT: U 31 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8429 (tm-30) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.1857 time to fit residues: 32.7079 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.129191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110634 restraints weight = 11497.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112411 restraints weight = 7117.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113855 restraints weight = 5219.494| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7917 Z= 0.145 Angle : 0.551 9.773 10750 Z= 0.277 Chirality : 0.040 0.148 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.122 29.168 1066 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.39 % Allowed : 14.74 % Favored : 82.87 % 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: 1.45 (0.28), residues: 981 helix: 2.53 (0.22), residues: 568 sheet: -0.12 (0.84), residues: 41 loop : -1.53 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.013 0.001 PHE 9 7 TYR 0.020 0.002 TYR 9 95 ARG 0.002 0.000 ARG 9 105 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 445) hydrogen bonds : angle 3.80203 ( 1293) metal coordination : bond 0.01077 ( 8) metal coordination : angle 3.85255 ( 6) covalent geometry : bond 0.00347 ( 7908) covalent geometry : angle 0.54375 (10744) Misc. bond : bond 0.00036 ( 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 129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.901 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8535 (m-80) cc_final: 0.8137 (t80) REVERT: 2 324 LYS cc_start: 0.8166 (tttt) cc_final: 0.7919 (tttp) REVERT: 9 234 TYR cc_start: 0.8056 (t80) cc_final: 0.7291 (t80) REVERT: 9 238 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6685 (tp) REVERT: 9 497 MET cc_start: 0.8090 (ttp) cc_final: 0.7488 (ttt) REVERT: E 135 TYR cc_start: 0.6896 (t80) cc_final: 0.6646 (t80) REVERT: U 31 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8425 (tm-30) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.2076 time to fit residues: 34.2326 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.128840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109980 restraints weight = 11673.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111809 restraints weight = 7214.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113211 restraints weight = 5293.086| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1535 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= 0.151 Angle : 0.552 9.726 10750 Z= 0.280 Chirality : 0.040 0.142 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.158 29.411 1066 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.90 % Allowed : 14.99 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.28), residues: 981 helix: 2.52 (0.22), residues: 567 sheet: -0.34 (0.83), residues: 42 loop : -1.54 (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 0.020 0.002 TYR 2 296 ARG 0.002 0.000 ARG 9 105 Details of bonding type rmsd hydrogen bonds : bond 0.05111 ( 445) hydrogen bonds : angle 3.81763 ( 1293) metal coordination : bond 0.01184 ( 8) metal coordination : angle 3.98188 ( 6) covalent geometry : bond 0.00362 ( 7908) covalent geometry : angle 0.54445 (10744) Misc. bond : bond 0.00036 ( 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 133 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.893 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8521 (m-80) cc_final: 0.8126 (t80) REVERT: 2 324 LYS cc_start: 0.8206 (tttt) cc_final: 0.7946 (tttp) REVERT: 9 234 TYR cc_start: 0.8092 (t80) cc_final: 0.7338 (t80) REVERT: 9 238 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6703 (tp) REVERT: 9 265 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8464 (tt) REVERT: 9 497 MET cc_start: 0.8078 (ttp) cc_final: 0.7483 (ttt) REVERT: U 31 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 23 outliers final: 18 residues processed: 122 average time/residue: 0.1879 time to fit residues: 31.3716 Evaluate side-chains 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 208 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: 1.9990 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 0.0570 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.127362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108730 restraints weight = 11639.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110670 restraints weight = 7206.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111962 restraints weight = 5259.308| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7917 Z= 0.171 Angle : 0.588 10.847 10750 Z= 0.297 Chirality : 0.041 0.152 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.258 29.781 1066 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.02 % Allowed : 16.12 % 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 (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: 1.37 (0.28), residues: 981 helix: 2.47 (0.22), residues: 567 sheet: -0.35 (0.83), residues: 42 loop : -1.55 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.014 0.001 PHE 9 7 TYR 0.021 0.002 TYR 9 95 ARG 0.007 0.000 ARG 2 417 Details of bonding type rmsd hydrogen bonds : bond 0.05425 ( 445) hydrogen bonds : angle 3.89972 ( 1293) metal coordination : bond 0.01422 ( 8) metal coordination : angle 4.42187 ( 6) covalent geometry : bond 0.00417 ( 7908) covalent geometry : angle 0.57886 (10744) Misc. bond : bond 0.00044 ( 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 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.019 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8618 (m-80) cc_final: 0.8204 (t80) REVERT: 2 324 LYS cc_start: 0.8244 (tttt) cc_final: 0.7970 (tttp) REVERT: 9 234 TYR cc_start: 0.8124 (t80) cc_final: 0.7393 (t80) REVERT: 9 238 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6580 (tp) REVERT: 9 265 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8480 (tt) REVERT: 9 497 MET cc_start: 0.8098 (ttp) cc_final: 0.7546 (ttt) REVERT: U 31 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8391 (tm-30) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.1906 time to fit residues: 31.5954 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 : 0.901 ------------------------------------------------------------------------------- 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 208 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.127361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108587 restraints weight = 11834.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110545 restraints weight = 7276.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111822 restraints weight = 5264.984| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7917 Z= 0.170 Angle : 0.589 10.644 10750 Z= 0.299 Chirality : 0.041 0.171 1265 Planarity : 0.004 0.043 1346 Dihedral : 4.285 30.114 1066 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.02 % Allowed : 15.99 % 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 (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: 1.30 (0.28), residues: 981 helix: 2.42 (0.22), residues: 568 sheet: -0.38 (0.84), residues: 42 loop : -1.59 (0.31), residues: 371 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 0.014 0.001 PHE 9 7 TYR 0.021 0.002 TYR 9 95 ARG 0.002 0.000 ARG 9 105 Details of bonding type rmsd hydrogen bonds : bond 0.05392 ( 445) hydrogen bonds : angle 3.90085 ( 1293) metal coordination : bond 0.01376 ( 8) metal coordination : angle 4.32286 ( 6) covalent geometry : bond 0.00415 ( 7908) covalent geometry : angle 0.58013 (10744) Misc. bond : bond 0.00047 ( 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 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.988 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8615 (m-80) cc_final: 0.8198 (t80) REVERT: 2 324 LYS cc_start: 0.8221 (tttt) cc_final: 0.7957 (tttp) REVERT: 9 234 TYR cc_start: 0.8112 (t80) cc_final: 0.7375 (t80) REVERT: 9 238 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6570 (tp) REVERT: 9 265 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8456 (tt) REVERT: 9 497 MET cc_start: 0.8104 (ttp) cc_final: 0.7547 (ttt) REVERT: U 31 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8382 (tm-30) outliers start: 24 outliers final: 21 residues processed: 118 average time/residue: 0.1934 time to fit residues: 31.6273 Evaluate side-chains 126 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain U residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.0370 chunk 28 optimal weight: 0.0470 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.130501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111449 restraints weight = 11748.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113491 restraints weight = 7052.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114965 restraints weight = 5035.891| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7917 Z= 0.129 Angle : 0.555 10.058 10750 Z= 0.283 Chirality : 0.040 0.176 1265 Planarity : 0.004 0.044 1346 Dihedral : 4.093 29.724 1066 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: 1.41 (0.28), residues: 981 helix: 2.48 (0.22), residues: 572 sheet: -0.21 (0.84), residues: 41 loop : -1.55 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 105 HIS 0.003 0.001 HIS E 33 PHE 0.011 0.001 PHE 9 7 TYR 0.017 0.001 TYR 9 159 ARG 0.002 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 445) hydrogen bonds : angle 3.73336 ( 1293) metal coordination : bond 0.01032 ( 8) metal coordination : angle 3.74535 ( 6) covalent geometry : bond 0.00300 ( 7908) covalent geometry : angle 0.54853 (10744) Misc. bond : bond 0.00026 ( 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 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.941 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8540 (m-80) cc_final: 0.8186 (t80) REVERT: 2 324 LYS cc_start: 0.8142 (tttt) cc_final: 0.7906 (tttp) REVERT: 9 234 TYR cc_start: 0.7999 (t80) cc_final: 0.7278 (t80) REVERT: 9 238 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6486 (tp) REVERT: 9 265 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8441 (tt) REVERT: 9 497 MET cc_start: 0.8062 (ttp) cc_final: 0.7489 (ttt) REVERT: E 106 MET cc_start: 0.7486 (ptp) cc_final: 0.7000 (ptp) REVERT: U 31 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8417 (tm-30) outliers start: 20 outliers final: 18 residues processed: 120 average time/residue: 0.1995 time to fit residues: 32.9077 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 : 1.056 ------------------------------------------------------------------------------- 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 208 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.130286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111511 restraints weight = 11611.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113548 restraints weight = 7173.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114696 restraints weight = 5193.394| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7917 Z= 0.133 Angle : 0.557 9.767 10750 Z= 0.283 Chirality : 0.039 0.168 1265 Planarity : 0.004 0.043 1346 Dihedral : 4.069 28.565 1066 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.90 % Allowed : 16.50 % Favored : 80.60 % 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: 2.55 (0.22), residues: 567 sheet: -0.20 (0.84), residues: 41 loop : -1.53 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 105 HIS 0.002 0.001 HIS E 33 PHE 0.012 0.001 PHE 9 7 TYR 0.018 0.001 TYR 9 95 ARG 0.002 0.000 ARG 9 105 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 445) hydrogen bonds : angle 3.73047 ( 1293) metal coordination : bond 0.01123 ( 8) metal coordination : angle 3.78653 ( 6) covalent geometry : bond 0.00311 ( 7908) covalent geometry : angle 0.54997 (10744) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.32 seconds wall clock time: 43 minutes 45.88 seconds (2625.88 seconds total)