Starting phenix.real_space_refine on Sat Apr 6 08:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmq_17764/04_2024/8pmq_17764_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmq_17764/04_2024/8pmq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmq_17764/04_2024/8pmq_17764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmq_17764/04_2024/8pmq_17764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmq_17764/04_2024/8pmq_17764_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmq_17764/04_2024/8pmq_17764_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.88, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 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... running ksdssp... Secondary structure from input PDB file: 42 helices and 4 sheets defined 54.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain '2' and resid 3 through 14 removed outlier: 3.668A pdb=" N ALA 2 13 " --> pdb=" O GLU 2 9 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS 2 14 " --> pdb=" O THR 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 27 through 54 Processing helix chain '2' and resid 70 through 113 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) removed outlier: 4.174A pdb=" N ASN 2 112 " --> pdb=" O LYS 2 108 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS 2 113 " --> pdb=" O SER 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 119 through 122 Processing helix chain '2' and resid 129 through 145 removed outlier: 4.034A pdb=" N MET 2 132 " --> pdb=" O LYS 2 129 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU 2 133 " --> pdb=" O GLU 2 130 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN 2 136 " --> pdb=" O GLU 2 133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA 2 138 " --> pdb=" O VAL 2 135 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE 2 139 " --> pdb=" O ASN 2 136 " (cutoff:3.500A) Processing helix chain '2' and resid 159 through 165 Processing helix chain '2' and resid 175 through 189 removed outlier: 3.583A pdb=" N LYS 2 189 " --> pdb=" O HIS 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 193 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 210 through 225 Processing helix chain '2' and resid 280 through 299 Processing helix chain '2' and resid 307 through 331 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 350 through 352 No H-bonds generated for 'chain '2' and resid 350 through 352' Processing helix chain '2' and resid 386 through 391 Processing helix chain '9' and resid 12 through 18 Processing helix chain '9' and resid 21 through 60 Proline residue: 9 26 - end of helix removed outlier: 3.589A pdb=" N GLU 9 60 " --> pdb=" O ASN 9 56 " (cutoff:3.500A) Processing helix chain '9' and resid 64 through 115 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 153 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 169 through 176 Processing helix chain '9' and resid 180 through 182 No H-bonds generated for 'chain '9' and resid 180 through 182' Processing helix chain '9' and resid 187 through 199 Processing helix chain '9' and resid 205 through 213 Processing helix chain '9' and resid 215 through 221 Processing helix chain '9' and resid 226 through 239 Processing helix chain '9' and resid 243 through 253 Processing helix chain '9' and resid 255 through 257 No H-bonds generated for 'chain '9' and resid 255 through 257' Processing helix chain '9' and resid 263 through 270 Processing helix chain '9' and resid 348 through 351 No H-bonds generated for 'chain '9' and resid 348 through 351' Processing helix chain '9' and resid 353 through 371 removed outlier: 3.743A pdb=" N ASP 9 361 " --> pdb=" O VAL 9 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 9 362 " --> pdb=" O LEU 9 359 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR 9 371 " --> pdb=" O TYR 9 368 " (cutoff:3.500A) Processing helix chain '9' and resid 378 through 389 removed outlier: 3.655A pdb=" N SER 9 388 " --> pdb=" O SER 9 384 " (cutoff:3.500A) Processing helix chain '9' and resid 422 through 428 Processing helix chain '9' and resid 442 through 447 Processing helix chain '9' and resid 473 through 485 Processing helix chain '9' and resid 507 through 509 No H-bonds generated for 'chain '9' and resid 507 through 509' Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 87 through 90 No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 99 through 111 Proline residue: E 108 - end of helix Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 134 through 146 Processing helix chain 'E' and resid 149 through 155 Processing helix chain 'U' and resid 23 through 34 Processing helix chain 'U' and resid 38 through 40 No H-bonds generated for 'chain 'U' and resid 38 through 40' Processing sheet with id= A, first strand: chain '9' and resid 462 through 464 Processing sheet with id= B, 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= C, first strand: chain 'E' and resid 22 through 24 Processing sheet with id= D, first strand: chain 'U' and resid 12 through 16 385 hydrogen bonds defined for protein. 1080 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: 1.79 Time building geometry restraints manager: 3.29 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: 100.12 - 106.95: 222 106.95 - 113.77: 4585 113.77 - 120.59: 3216 120.59 - 127.41: 2643 127.41 - 134.24: 78 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: 1.50 - 2.18: 1 2.18 - 2.86: 2704 2.86 - 3.54: 10890 3.54 - 4.22: 16122 4.22 - 4.90: 29244 Nonbonded interactions: 58961 Sorted by model distance: nonbonded pdb=" NZ LYS E 85 " pdb=" C GLY U 76 " model vdw 1.498 3.350 nonbonded pdb=" O PRO 2 362 " pdb=" NZ LYS 2 365 " model vdw 2.266 2.520 nonbonded pdb=" O GLU 9 162 " pdb=" OG1 THR 9 163 " model vdw 2.316 2.440 nonbonded pdb=" NZ LYS 9 215 " pdb=" OE2 GLU 9 226 " model vdw 2.341 2.520 nonbonded pdb=" OE2 GLU 2 341 " pdb=" ND1 HIS 9 452 " model vdw 2.342 2.520 ... (remaining 58956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 4.420 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.230 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- 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= 0.344 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 : 1.498 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 fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.922 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: 0.2179 time to fit residues: 39.5659 Evaluate side-chains 108 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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: 0.8980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 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 U 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0996 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= 0.281 Angle : 0.565 11.720 10744 Z= 0.285 Chirality : 0.041 0.155 1265 Planarity : 0.004 0.048 1346 Dihedral : 4.992 52.820 1070 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.89 % Allowed : 9.07 % Favored : 89.04 % 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: 0.92 (0.28), residues: 981 helix: 1.96 (0.22), residues: 560 sheet: 0.26 (0.87), residues: 39 loop : -1.50 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 9 210 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 0.000 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 fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.886 Fit side-chains REVERT: 2 49 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7816 (tptp) REVERT: E 135 TYR cc_start: 0.6683 (t80) cc_final: 0.6474 (t80) outliers start: 15 outliers final: 13 residues processed: 120 average time/residue: 0.2132 time to fit residues: 34.8598 Evaluate side-chains 118 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 2 residue 72 ARG Chi-restraints excluded: chain 2 residue 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 8 ASN 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 49 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7908 Z= 0.316 Angle : 0.575 11.318 10744 Z= 0.291 Chirality : 0.041 0.180 1265 Planarity : 0.004 0.042 1346 Dihedral : 4.859 55.907 1070 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.02 % Allowed : 12.47 % Favored : 84.51 % 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: 0.73 (0.27), residues: 981 helix: 1.85 (0.22), residues: 560 sheet: 0.10 (0.86), residues: 39 loop : -1.65 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 210 HIS 0.003 0.001 HIS E 33 PHE 0.014 0.002 PHE 9 7 TYR 0.022 0.002 TYR 9 95 ARG 0.005 0.001 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 fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.909 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8516 (m-80) cc_final: 0.8067 (t80) REVERT: 9 436 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9132 (p) REVERT: 9 497 MET cc_start: 0.7897 (ttp) cc_final: 0.7275 (ttt) outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 0.1999 time to fit residues: 31.9380 Evaluate side-chains 117 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 39 GLN 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 8 ASN 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 351 LEU Chi-restraints excluded: chain 9 residue 436 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 320 GLN U 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1325 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= 0.277 Angle : 0.553 11.241 10744 Z= 0.280 Chirality : 0.041 0.150 1265 Planarity : 0.004 0.041 1346 Dihedral : 4.431 31.695 1066 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.15 % Allowed : 13.98 % 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: 0.78 (0.28), residues: 981 helix: 1.91 (0.22), residues: 561 sheet: 0.06 (0.85), residues: 39 loop : -1.64 (0.31), residues: 381 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 0.005 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 132 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.964 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8492 (m-80) cc_final: 0.8074 (t80) REVERT: 2 329 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7928 (tpp80) REVERT: 9 224 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8436 (pp) REVERT: 9 497 MET cc_start: 0.8010 (ttp) cc_final: 0.7487 (ttt) outliers start: 25 outliers final: 21 residues processed: 120 average time/residue: 0.2550 time to fit residues: 42.8370 Evaluate side-chains 126 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 26 LEU Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 8 ASN 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 204 LEU 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 79 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7908 Z= 0.205 Angle : 0.514 10.945 10744 Z= 0.260 Chirality : 0.039 0.194 1265 Planarity : 0.004 0.040 1346 Dihedral : 4.210 30.559 1066 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.77 % Allowed : 15.49 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.28), residues: 981 helix: 2.02 (0.23), residues: 563 sheet: 0.12 (0.86), residues: 39 loop : -1.53 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 105 HIS 0.003 0.001 HIS 2 142 PHE 0.013 0.001 PHE 9 7 TYR 0.017 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 139 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.994 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8480 (m-80) cc_final: 0.8083 (t80) REVERT: 9 174 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8730 (mt) REVERT: 9 224 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8468 (pp) REVERT: 9 497 MET cc_start: 0.8038 (ttp) cc_final: 0.7526 (ttt) REVERT: U 33 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8543 (tttp) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 0.2278 time to fit residues: 40.1391 Evaluate side-chains 124 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 174 LEU Chi-restraints excluded: chain 9 residue 204 LEU 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 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1437 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= 0.223 Angle : 0.525 11.009 10744 Z= 0.264 Chirality : 0.040 0.209 1265 Planarity : 0.004 0.041 1346 Dihedral : 4.201 29.547 1066 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.65 % Allowed : 15.62 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.28), residues: 981 helix: 2.01 (0.22), residues: 563 sheet: 0.15 (0.86), residues: 39 loop : -1.52 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 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 135 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.938 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8504 (m-80) cc_final: 0.8108 (t80) REVERT: 9 224 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8486 (pp) REVERT: 9 265 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8538 (tt) REVERT: 9 497 MET cc_start: 0.8054 (ttp) cc_final: 0.7520 (ttt) REVERT: E 118 ASP cc_start: 0.6719 (p0) cc_final: 0.6406 (p0) outliers start: 29 outliers final: 20 residues processed: 123 average time/residue: 0.1997 time to fit residues: 34.3481 Evaluate side-chains 127 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 26 LEU Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 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 204 LEU Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE 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 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 0.0010 chunk 58 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 GLN ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.002 0.027 7908 Z= 0.161 Angle : 0.489 10.931 10744 Z= 0.246 Chirality : 0.038 0.182 1265 Planarity : 0.003 0.041 1346 Dihedral : 3.980 28.790 1066 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 1.11 (0.28), residues: 981 helix: 2.13 (0.23), residues: 565 sheet: 0.37 (0.87), residues: 38 loop : -1.48 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 105 HIS 0.003 0.001 HIS 2 142 PHE 0.011 0.001 PHE 9 7 TYR 0.015 0.001 TYR 2 296 ARG 0.002 0.000 ARG E 6 *********************** 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 134 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.952 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8423 (m-80) cc_final: 0.8079 (t80) REVERT: 2 187 LEU cc_start: 0.8259 (tp) cc_final: 0.8004 (tt) REVERT: 9 59 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: 9 224 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8455 (pp) REVERT: 9 234 TYR cc_start: 0.7927 (t80) cc_final: 0.7279 (t80) REVERT: 9 265 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8497 (tt) REVERT: 9 497 MET cc_start: 0.7915 (ttp) cc_final: 0.7366 (ttt) REVERT: E 118 ASP cc_start: 0.6677 (p0) cc_final: 0.6389 (p0) outliers start: 22 outliers final: 19 residues processed: 125 average time/residue: 0.2140 time to fit residues: 37.1532 Evaluate side-chains 128 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 26 LEU Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 59 PHE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 204 LEU Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 395 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7908 Z= 0.307 Angle : 0.574 11.147 10744 Z= 0.288 Chirality : 0.041 0.203 1265 Planarity : 0.004 0.040 1346 Dihedral : 4.296 28.848 1066 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.53 % Allowed : 16.50 % Favored : 79.97 % 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: 0.88 (0.28), residues: 981 helix: 1.97 (0.22), residues: 563 sheet: -0.57 (0.75), residues: 49 loop : -1.53 (0.32), residues: 369 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 0.004 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 131 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.915 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8526 (m-80) cc_final: 0.8068 (t80) REVERT: 2 187 LEU cc_start: 0.8315 (tp) cc_final: 0.8056 (tt) REVERT: 9 59 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: 9 224 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8511 (pp) REVERT: 9 497 MET cc_start: 0.8152 (ttp) cc_final: 0.7657 (ttt) outliers start: 28 outliers final: 23 residues processed: 120 average time/residue: 0.1921 time to fit residues: 31.7806 Evaluate side-chains 127 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 26 LEU Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 59 PHE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 196 THR Chi-restraints excluded: chain 9 residue 204 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.0010 chunk 57 optimal weight: 0.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 GLN ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7908 Z= 0.186 Angle : 0.518 11.795 10744 Z= 0.260 Chirality : 0.039 0.181 1265 Planarity : 0.003 0.039 1346 Dihedral : 4.051 29.586 1066 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.02 % Allowed : 17.25 % Favored : 79.72 % 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: 1.02 (0.28), residues: 981 helix: 2.05 (0.23), residues: 567 sheet: -0.45 (0.76), residues: 48 loop : -1.46 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 105 HIS 0.003 0.001 HIS 2 142 PHE 0.012 0.001 PHE 9 7 TYR 0.016 0.001 TYR 9 27 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 131 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: 2 8 PHE cc_start: 0.8548 (m-80) cc_final: 0.8196 (t80) REVERT: 2 187 LEU cc_start: 0.8264 (tp) cc_final: 0.8007 (tt) REVERT: 2 331 LEU cc_start: 0.8131 (mp) cc_final: 0.7906 (mp) REVERT: 9 59 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: 9 224 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8468 (pp) REVERT: 9 265 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8506 (tt) REVERT: 9 497 MET cc_start: 0.8008 (ttp) cc_final: 0.7452 (ttt) REVERT: E 118 ASP cc_start: 0.6525 (p0) cc_final: 0.6288 (p0) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.1920 time to fit residues: 32.4988 Evaluate side-chains 128 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 26 LEU Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 59 PHE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 204 LEU Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 459 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain U residue 4 PHE 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 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 46 HIS U 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7908 Z= 0.335 Angle : 0.586 10.902 10744 Z= 0.297 Chirality : 0.042 0.215 1265 Planarity : 0.004 0.040 1346 Dihedral : 4.392 29.103 1066 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.40 % Allowed : 16.88 % Favored : 79.72 % 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: 0.77 (0.28), residues: 981 helix: 1.88 (0.22), residues: 563 sheet: -1.11 (0.70), residues: 59 loop : -1.50 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 105 HIS 0.003 0.001 HIS 2 142 PHE 0.015 0.001 PHE 9 7 TYR 0.021 0.002 TYR 9 95 ARG 0.004 0.000 ARG 9 105 ********************** 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 128 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.927 Fit side-chains REVERT: 2 8 PHE cc_start: 0.8543 (m-80) cc_final: 0.8062 (t80) REVERT: 2 187 LEU cc_start: 0.8305 (tp) cc_final: 0.8047 (tt) REVERT: 9 59 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: 9 224 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8538 (pp) REVERT: 9 265 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8501 (tt) REVERT: 9 497 MET cc_start: 0.8003 (ttp) cc_final: 0.7403 (ttt) outliers start: 27 outliers final: 24 residues processed: 117 average time/residue: 0.1956 time to fit residues: 31.9429 Evaluate side-chains 127 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 26 LEU Chi-restraints excluded: chain 2 residue 39 GLN Chi-restraints excluded: chain 2 residue 46 HIS Chi-restraints excluded: chain 2 residue 81 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 2 residue 203 MET Chi-restraints excluded: chain 2 residue 211 THR Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 346 VAL Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 59 PHE Chi-restraints excluded: chain 9 residue 96 CYS Chi-restraints excluded: chain 9 residue 145 ILE Chi-restraints excluded: chain 9 residue 196 THR Chi-restraints excluded: chain 9 residue 204 LEU Chi-restraints excluded: chain 9 residue 224 ILE Chi-restraints excluded: chain 9 residue 238 LEU Chi-restraints excluded: chain 9 residue 265 LEU Chi-restraints excluded: chain 9 residue 351 LEU Chi-restraints excluded: chain 9 residue 395 CYS Chi-restraints excluded: chain 9 residue 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 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107492 restraints weight = 11555.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109426 restraints weight = 7235.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110709 restraints weight = 5284.788| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1595 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= 0.261 Angle : 0.559 10.977 10744 Z= 0.282 Chirality : 0.040 0.197 1265 Planarity : 0.004 0.039 1346 Dihedral : 4.299 29.375 1066 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.53 % Allowed : 16.75 % Favored : 79.72 % 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: 0.82 (0.28), residues: 981 helix: 1.93 (0.22), residues: 562 sheet: -0.77 (0.75), residues: 49 loop : -1.52 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.65 seconds wall clock time: 32 minutes 35.22 seconds (1955.22 seconds total)