Starting phenix.real_space_refine on Sun Jul 21 04:30:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6o_41073/07_2024/8t6o_41073.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6o_41073/07_2024/8t6o_41073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6o_41073/07_2024/8t6o_41073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6o_41073/07_2024/8t6o_41073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6o_41073/07_2024/8t6o_41073.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6o_41073/07_2024/8t6o_41073.cif" } resolution = 3.1 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1668 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 19 5.16 5 C 7106 2.51 5 N 2080 2.21 5 O 2569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 757": "OE1" <-> "OE2" Residue "A GLU 1205": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11904 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 9151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 9151 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 32, 'TRANS': 1104} Chain breaks: 3 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1854 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 41, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 74} Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 443 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Time building chain proxies: 8.52, per 1000 atoms: 0.72 Number of scatterers: 11904 At special positions: 0 Unit cell: (88.3192, 123.314, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 130 15.00 O 2569 8.00 N 2080 7.00 C 7106 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: 6.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 56.6% alpha, 8.8% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.085A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.819A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.510A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.028A pdb=" N GLY A 205 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.631A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 381 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.552A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.558A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.918A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.724A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.800A pdb=" N VAL A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.532A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.522A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.567A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.538A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 removed outlier: 3.854A pdb=" N HIS A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.692A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 removed outlier: 3.564A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.699A pdb=" N TYR A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.594A pdb=" N PHE A1258 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A1259 " --> pdb=" O LYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 4.758A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1311 Processing helix chain 'A' and resid 1312 through 1315 Processing helix chain 'A' and resid 1339 through 1343 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 4.599A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.052A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A1346 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.934A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.614A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.472A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A1109 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1157 through 1167 Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.966A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.30: 1680 1.30 - 1.53: 9548 1.53 - 1.76: 1134 1.76 - 1.99: 36 1.99 - 2.21: 1 Bond restraints: 12399 Sorted by residual: bond pdb=" CB PRO A 731 " pdb=" CG PRO A 731 " ideal model delta sigma weight residual 1.492 2.214 -0.722 5.00e-02 4.00e+02 2.09e+02 bond pdb=" CG PRO A 731 " pdb=" CD PRO A 731 " ideal model delta sigma weight residual 1.503 1.073 0.430 3.40e-02 8.65e+02 1.60e+02 bond pdb=" C ASN A 199 " pdb=" O ASN A 199 " ideal model delta sigma weight residual 1.235 1.252 -0.018 4.70e-03 4.53e+04 1.40e+01 bond pdb=" N PRO A 731 " pdb=" CA PRO A 731 " ideal model delta sigma weight residual 1.469 1.426 0.043 1.28e-02 6.10e+03 1.13e+01 bond pdb=" N ASN A 692 " pdb=" CA ASN A 692 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.20e+00 ... (remaining 12394 not shown) Histogram of bond angle deviations from ideal: 34.25 - 56.22: 1 56.22 - 78.18: 1 78.18 - 100.15: 20 100.15 - 122.11: 15017 122.11 - 144.07: 2286 Bond angle restraints: 17325 Sorted by residual: angle pdb=" CA PRO A 731 " pdb=" N PRO A 731 " pdb=" CD PRO A 731 " ideal model delta sigma weight residual 112.00 77.83 34.17 1.40e+00 5.10e-01 5.96e+02 angle pdb=" CB PRO A 731 " pdb=" CG PRO A 731 " pdb=" CD PRO A 731 " ideal model delta sigma weight residual 106.10 34.25 71.85 3.20e+00 9.77e-02 5.04e+02 angle pdb=" N PRO A 731 " pdb=" CD PRO A 731 " pdb=" CG PRO A 731 " ideal model delta sigma weight residual 103.20 118.98 -15.78 1.50e+00 4.44e-01 1.11e+02 angle pdb=" N PRO A 731 " pdb=" CA PRO A 731 " pdb=" CB PRO A 731 " ideal model delta sigma weight residual 103.25 93.31 9.94 1.05e+00 9.07e-01 8.96e+01 angle pdb=" CA LYS A1325 " pdb=" CB LYS A1325 " pdb=" CG LYS A1325 " ideal model delta sigma weight residual 114.10 126.34 -12.24 2.00e+00 2.50e-01 3.75e+01 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.00: 6874 29.00 - 58.00: 512 58.00 - 87.00: 119 87.00 - 116.00: 8 116.00 - 145.00: 2 Dihedral angle restraints: 7515 sinusoidal: 4171 harmonic: 3344 Sorted by residual: dihedral pdb=" N PRO A 731 " pdb=" CG PRO A 731 " pdb=" CD PRO A 731 " pdb=" CB PRO A 731 " ideal model delta sinusoidal sigma weight residual 30.00 117.77 -87.77 1 1.50e+01 4.44e-03 4.10e+01 dihedral pdb=" CA LEU A1266 " pdb=" C LEU A1266 " pdb=" N ASP A1267 " pdb=" CA ASP A1267 " 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 GLU A1271 " pdb=" C GLU A1271 " pdb=" N GLN A1272 " pdb=" CA GLN A1272 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1616 0.066 - 0.133: 334 0.133 - 0.199: 48 0.199 - 0.265: 8 0.265 - 0.331: 3 Chirality restraints: 2009 Sorted by residual: chirality pdb=" CA PRO A 731 " pdb=" N PRO A 731 " pdb=" C PRO A 731 " pdb=" CB PRO A 731 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CG LEU A 244 " pdb=" CB LEU A 244 " pdb=" CD1 LEU A 244 " pdb=" CD2 LEU A 244 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2006 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " -0.098 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO A 731 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 645 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" CG ASP A 645 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASP A 645 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP A 645 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 25 " 0.049 2.00e-02 2.50e+03 1.97e-02 1.16e+01 pdb=" N9 DG D 25 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG D 25 " -0.017 2.00e-02 2.50e+03 pdb=" N7 DG D 25 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG D 25 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG D 25 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG D 25 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG D 25 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG D 25 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG D 25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG D 25 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG D 25 " -0.009 2.00e-02 2.50e+03 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1367 2.75 - 3.29: 11611 3.29 - 3.83: 21331 3.83 - 4.36: 25091 4.36 - 4.90: 39284 Nonbonded interactions: 98684 Sorted by model distance: nonbonded pdb=" OG1 THR A 525 " pdb=" OD1 ASN A 690 " model vdw 2.217 2.440 nonbonded pdb=" O LEU A1266 " pdb=" OH TYR A1294 " model vdw 2.229 2.440 nonbonded pdb=" O TYR A1237 " pdb=" OG SER A1240 " model vdw 2.301 2.440 nonbonded pdb=" O LEU A1291 " pdb=" ND2 ASN A1295 " model vdw 2.313 2.520 nonbonded pdb=" OD1 ASN A 609 " pdb=" OE1 GLU A 611 " model vdw 2.328 3.040 ... (remaining 98679 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 45.910 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.009 0.722 12399 Z= 0.697 Angle : 1.230 71.848 17325 Z= 0.624 Chirality : 0.055 0.331 2009 Planarity : 0.006 0.123 1736 Dihedral : 19.518 145.001 5347 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.41 % Allowed : 13.53 % Favored : 86.06 % Cbeta Deviations : 0.09 % 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 (0.23), residues: 1129 helix: -0.76 (0.19), residues: 574 sheet: -0.19 (0.43), residues: 118 loop : -0.63 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A1136 HIS 0.013 0.002 HIS A1264 PHE 0.035 0.003 PHE A1046 TYR 0.030 0.003 TYR A 25 ARG 0.012 0.001 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8769 (m-40) cc_final: 0.7678 (m-40) REVERT: A 263 LYS cc_start: 0.9397 (tttp) cc_final: 0.8993 (mmtt) REVERT: A 304 ASP cc_start: 0.8845 (m-30) cc_final: 0.8608 (m-30) REVERT: A 370 GLU cc_start: 0.7919 (tt0) cc_final: 0.7226 (tm-30) REVERT: A 696 LEU cc_start: 0.8439 (mt) cc_final: 0.8226 (mt) REVERT: A 1189 GLU cc_start: 0.8699 (tp30) cc_final: 0.8351 (tp30) REVERT: A 1312 LEU cc_start: 0.8925 (tp) cc_final: 0.8655 (mt) outliers start: 4 outliers final: 0 residues processed: 133 average time/residue: 0.2637 time to fit residues: 51.0379 Evaluate side-chains 104 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 0.0070 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 255 ASN A 609 ASN A 726 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 12399 Z= 0.324 Angle : 0.678 8.037 17325 Z= 0.364 Chirality : 0.040 0.164 2009 Planarity : 0.004 0.072 1736 Dihedral : 20.905 141.693 3042 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.24 % Allowed : 11.80 % Favored : 85.96 % 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: -0.20 (0.24), residues: 1129 helix: 0.33 (0.21), residues: 582 sheet: -0.30 (0.43), residues: 118 loop : -0.54 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 464 HIS 0.006 0.001 HIS A 129 PHE 0.018 0.002 PHE A1313 TYR 0.021 0.002 TYR A 362 ARG 0.005 0.001 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8593 (tp30) cc_final: 0.8240 (tp30) REVERT: A 251 ASN cc_start: 0.8837 (m-40) cc_final: 0.7569 (m-40) REVERT: A 263 LYS cc_start: 0.9439 (tttp) cc_final: 0.8992 (mmtt) REVERT: A 465 MET cc_start: 0.8976 (ppp) cc_final: 0.8775 (ppp) REVERT: A 560 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6355 (t) REVERT: A 634 GLU cc_start: 0.8829 (tp30) cc_final: 0.8623 (tm-30) REVERT: A 763 MET cc_start: 0.9000 (tpp) cc_final: 0.8400 (mtp) REVERT: A 930 HIS cc_start: 0.8579 (m90) cc_final: 0.8376 (m90) REVERT: A 1089 MET cc_start: 0.8974 (ttm) cc_final: 0.8749 (ttp) REVERT: A 1125 ASP cc_start: 0.8442 (t0) cc_final: 0.8171 (t0) REVERT: A 1180 ASP cc_start: 0.8989 (t0) cc_final: 0.8740 (t0) REVERT: A 1356 TYR cc_start: 0.8498 (m-10) cc_final: 0.8131 (m-80) outliers start: 22 outliers final: 9 residues processed: 122 average time/residue: 0.2156 time to fit residues: 39.6649 Evaluate side-chains 103 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 122 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12399 Z= 0.184 Angle : 0.570 11.270 17325 Z= 0.307 Chirality : 0.038 0.162 2009 Planarity : 0.003 0.052 1736 Dihedral : 20.872 143.157 3042 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.24 % Allowed : 12.92 % Favored : 84.84 % 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: 0.31 (0.25), residues: 1129 helix: 0.87 (0.22), residues: 579 sheet: -0.16 (0.44), residues: 119 loop : -0.47 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.004 0.001 HIS A 129 PHE 0.012 0.001 PHE A 491 TYR 0.015 0.001 TYR A 362 ARG 0.005 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8501 (tp30) cc_final: 0.8100 (tp30) REVERT: A 251 ASN cc_start: 0.8806 (m-40) cc_final: 0.7324 (m-40) REVERT: A 263 LYS cc_start: 0.9422 (tttp) cc_final: 0.8971 (mmtt) REVERT: A 634 GLU cc_start: 0.8806 (tp30) cc_final: 0.8559 (tm-30) REVERT: A 746 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: A 930 HIS cc_start: 0.8506 (m90) cc_final: 0.8219 (m90) REVERT: A 1043 MET cc_start: 0.8025 (pmm) cc_final: 0.6761 (tmm) REVERT: A 1125 ASP cc_start: 0.8429 (t0) cc_final: 0.8143 (t0) REVERT: A 1180 ASP cc_start: 0.8948 (t0) cc_final: 0.8691 (t0) REVERT: A 1189 GLU cc_start: 0.8730 (tp30) cc_final: 0.8293 (tp30) REVERT: A 1356 TYR cc_start: 0.8566 (m-10) cc_final: 0.8211 (m-80) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 0.2112 time to fit residues: 37.1025 Evaluate side-chains 102 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 76 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN A 990 ASN A1308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12399 Z= 0.151 Angle : 0.543 8.392 17325 Z= 0.287 Chirality : 0.037 0.184 2009 Planarity : 0.003 0.046 1736 Dihedral : 20.677 147.017 3042 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.54 % Allowed : 12.82 % Favored : 84.64 % 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: 0.66 (0.25), residues: 1129 helix: 1.17 (0.22), residues: 582 sheet: -0.05 (0.46), residues: 117 loop : -0.33 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.004 0.001 HIS A1264 PHE 0.010 0.001 PHE A 966 TYR 0.018 0.001 TYR A 362 ARG 0.004 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8374 (tp30) cc_final: 0.7921 (tp30) REVERT: A 251 ASN cc_start: 0.8708 (m-40) cc_final: 0.8445 (m-40) REVERT: A 263 LYS cc_start: 0.9426 (tttp) cc_final: 0.9146 (mtpp) REVERT: A 634 GLU cc_start: 0.8782 (tp30) cc_final: 0.8547 (tm-30) REVERT: A 746 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 762 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6412 (tm-30) REVERT: A 763 MET cc_start: 0.9061 (tpp) cc_final: 0.8434 (ttp) REVERT: A 930 HIS cc_start: 0.8600 (m90) cc_final: 0.8178 (m90) REVERT: A 1043 MET cc_start: 0.8024 (pmm) cc_final: 0.6801 (tmm) REVERT: A 1125 ASP cc_start: 0.8428 (t0) cc_final: 0.8167 (t0) REVERT: A 1180 ASP cc_start: 0.8943 (t0) cc_final: 0.8694 (t0) REVERT: A 1189 GLU cc_start: 0.8767 (tp30) cc_final: 0.8308 (tp30) REVERT: A 1352 ILE cc_start: 0.9272 (tp) cc_final: 0.9031 (tp) outliers start: 25 outliers final: 9 residues processed: 122 average time/residue: 0.2414 time to fit residues: 43.1270 Evaluate side-chains 93 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 726 ASN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12399 Z= 0.241 Angle : 0.569 9.078 17325 Z= 0.301 Chirality : 0.038 0.198 2009 Planarity : 0.003 0.051 1736 Dihedral : 20.662 147.873 3042 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.54 % Allowed : 12.92 % Favored : 84.54 % 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: 0.71 (0.25), residues: 1129 helix: 1.24 (0.22), residues: 585 sheet: 0.08 (0.47), residues: 114 loop : -0.39 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.013 0.001 PHE A1324 TYR 0.018 0.001 TYR A 362 ARG 0.005 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8467 (tp30) cc_final: 0.8025 (tp30) REVERT: A 251 ASN cc_start: 0.8728 (m-40) cc_final: 0.8211 (m-40) REVERT: A 261 ASP cc_start: 0.8830 (p0) cc_final: 0.8546 (p0) REVERT: A 263 LYS cc_start: 0.9440 (tttp) cc_final: 0.9144 (mtpp) REVERT: A 304 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8529 (m-30) REVERT: A 634 GLU cc_start: 0.8797 (tp30) cc_final: 0.8566 (tm-30) REVERT: A 746 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: A 762 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 1043 MET cc_start: 0.8006 (pmm) cc_final: 0.6769 (tmm) REVERT: A 1125 ASP cc_start: 0.8470 (t0) cc_final: 0.8129 (t0) REVERT: A 1180 ASP cc_start: 0.8971 (t0) cc_final: 0.8727 (t0) REVERT: A 1189 GLU cc_start: 0.8823 (tp30) cc_final: 0.8352 (tp30) REVERT: A 1352 ILE cc_start: 0.9312 (tp) cc_final: 0.9022 (tp) outliers start: 25 outliers final: 18 residues processed: 107 average time/residue: 0.2255 time to fit residues: 36.2256 Evaluate side-chains 100 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12399 Z= 0.230 Angle : 0.559 8.062 17325 Z= 0.297 Chirality : 0.037 0.161 2009 Planarity : 0.003 0.047 1736 Dihedral : 20.656 148.081 3042 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.64 % Allowed : 13.73 % Favored : 83.62 % 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: 0.77 (0.25), residues: 1129 helix: 1.37 (0.22), residues: 581 sheet: 0.05 (0.48), residues: 114 loop : -0.46 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.018 0.002 PHE A1258 TYR 0.018 0.001 TYR A 362 ARG 0.006 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8535 (tp30) cc_final: 0.8085 (tp30) REVERT: A 304 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: A 634 GLU cc_start: 0.8789 (tp30) cc_final: 0.8559 (tm-30) REVERT: A 746 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 762 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 1043 MET cc_start: 0.8072 (pmm) cc_final: 0.6860 (tmm) REVERT: A 1125 ASP cc_start: 0.8462 (t0) cc_final: 0.8095 (t0) REVERT: A 1180 ASP cc_start: 0.9007 (t0) cc_final: 0.8778 (t0) REVERT: A 1189 GLU cc_start: 0.8850 (tp30) cc_final: 0.8412 (tp30) REVERT: A 1352 ILE cc_start: 0.9303 (tp) cc_final: 0.8945 (tp) outliers start: 26 outliers final: 16 residues processed: 107 average time/residue: 0.2267 time to fit residues: 36.4698 Evaluate side-chains 98 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A 758 ASN A1241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12399 Z= 0.253 Angle : 0.564 8.033 17325 Z= 0.299 Chirality : 0.038 0.162 2009 Planarity : 0.003 0.047 1736 Dihedral : 20.665 149.911 3042 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.05 % Allowed : 14.04 % Favored : 82.91 % 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 (0.25), residues: 1129 helix: 1.40 (0.22), residues: 581 sheet: 0.06 (0.50), residues: 114 loop : -0.51 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 PHE 0.013 0.001 PHE A 966 TYR 0.017 0.001 TYR A 362 ARG 0.004 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8560 (tp30) cc_final: 0.8119 (tp30) REVERT: A 304 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: A 494 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.9033 (ttm110) REVERT: A 557 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7520 (ttm170) REVERT: A 634 GLU cc_start: 0.8775 (tp30) cc_final: 0.8541 (tm-30) REVERT: A 746 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: A 762 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 959 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7945 (pttt) REVERT: A 1043 MET cc_start: 0.8076 (pmm) cc_final: 0.6695 (tmm) REVERT: A 1125 ASP cc_start: 0.8494 (t0) cc_final: 0.8113 (t0) REVERT: A 1180 ASP cc_start: 0.9020 (t0) cc_final: 0.8805 (t0) REVERT: A 1189 GLU cc_start: 0.8902 (tp30) cc_final: 0.8467 (tp30) REVERT: A 1352 ILE cc_start: 0.9309 (tp) cc_final: 0.8920 (tp) outliers start: 30 outliers final: 21 residues processed: 113 average time/residue: 0.2213 time to fit residues: 37.7319 Evaluate side-chains 110 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 12399 Z= 0.516 Angle : 0.759 7.331 17325 Z= 0.396 Chirality : 0.044 0.192 2009 Planarity : 0.005 0.052 1736 Dihedral : 21.025 146.301 3042 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 2.95 % Allowed : 14.95 % Favored : 82.10 % 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: -0.10 (0.24), residues: 1129 helix: 0.69 (0.21), residues: 587 sheet: -0.38 (0.48), residues: 116 loop : -0.95 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1074 HIS 0.011 0.002 HIS A 328 PHE 0.019 0.003 PHE A1324 TYR 0.019 0.002 TYR A 362 ARG 0.006 0.001 ARG A 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8758 (tp30) cc_final: 0.8334 (tp30) REVERT: A 220 ARG cc_start: 0.8631 (tpt90) cc_final: 0.8407 (tpt90) REVERT: A 494 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8723 (ttm110) REVERT: A 634 GLU cc_start: 0.8861 (tp30) cc_final: 0.8644 (tm-30) REVERT: A 746 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 762 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 959 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8143 (pttt) REVERT: A 1043 MET cc_start: 0.7860 (pmm) cc_final: 0.7553 (pmm) REVERT: A 1189 GLU cc_start: 0.8999 (tp30) cc_final: 0.8571 (tp30) REVERT: A 1228 LEU cc_start: 0.8571 (mt) cc_final: 0.8303 (mt) REVERT: A 1352 ILE cc_start: 0.9261 (tp) cc_final: 0.8861 (tp) outliers start: 29 outliers final: 22 residues processed: 108 average time/residue: 0.2473 time to fit residues: 39.1431 Evaluate side-chains 105 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 0.0020 chunk 118 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12399 Z= 0.164 Angle : 0.578 10.656 17325 Z= 0.300 Chirality : 0.038 0.221 2009 Planarity : 0.003 0.044 1736 Dihedral : 20.888 148.321 3042 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 2.34 % Allowed : 16.07 % Favored : 81.59 % 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: 0.48 (0.25), residues: 1129 helix: 1.21 (0.22), residues: 589 sheet: -0.13 (0.50), residues: 115 loop : -0.75 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.005 0.001 HIS A 167 PHE 0.016 0.001 PHE A1080 TYR 0.015 0.001 TYR A1201 ARG 0.005 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8567 (tp30) cc_final: 0.8120 (tp30) REVERT: A 304 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8523 (m-30) REVERT: A 557 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7715 (ttm170) REVERT: A 634 GLU cc_start: 0.8725 (tp30) cc_final: 0.8498 (tm-30) REVERT: A 712 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 746 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: A 762 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 959 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7933 (pttt) REVERT: A 1043 MET cc_start: 0.7970 (pmm) cc_final: 0.7713 (pmm) REVERT: A 1189 GLU cc_start: 0.8981 (tp30) cc_final: 0.8564 (tp30) REVERT: A 1352 ILE cc_start: 0.9275 (tp) cc_final: 0.8855 (tp) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.2638 time to fit residues: 42.6133 Evaluate side-chains 103 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12399 Z= 0.191 Angle : 0.574 10.559 17325 Z= 0.298 Chirality : 0.037 0.163 2009 Planarity : 0.003 0.048 1736 Dihedral : 20.769 151.269 3042 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 2.14 % Allowed : 16.68 % Favored : 81.18 % 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: 0.66 (0.25), residues: 1129 helix: 1.33 (0.22), residues: 587 sheet: -0.04 (0.51), residues: 115 loop : -0.61 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 723 PHE 0.011 0.001 PHE A1080 TYR 0.016 0.001 TYR A 362 ARG 0.004 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8528 (tp30) cc_final: 0.8062 (tp30) REVERT: A 304 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: A 557 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7659 (ttm170) REVERT: A 634 GLU cc_start: 0.8707 (tp30) cc_final: 0.8476 (tm-30) REVERT: A 712 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 746 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 762 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6460 (tm-30) REVERT: A 959 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7716 (pttt) REVERT: A 1043 MET cc_start: 0.8016 (pmm) cc_final: 0.6831 (tmm) REVERT: A 1189 GLU cc_start: 0.8999 (tp30) cc_final: 0.8605 (tp30) REVERT: A 1225 GLU cc_start: 0.8216 (pm20) cc_final: 0.7889 (pm20) REVERT: A 1352 ILE cc_start: 0.9301 (tp) cc_final: 0.8872 (tp) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.2459 time to fit residues: 38.5698 Evaluate side-chains 101 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 726 ASN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.103966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071824 restraints weight = 34139.961| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.25 r_work: 0.3124 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12399 Z= 0.211 Angle : 0.853 59.199 17325 Z= 0.489 Chirality : 0.037 0.273 2009 Planarity : 0.003 0.046 1736 Dihedral : 20.772 151.287 3042 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.93 % Allowed : 17.09 % Favored : 80.98 % Cbeta Deviations : 0.09 % 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 (0.25), residues: 1129 helix: 1.32 (0.22), residues: 587 sheet: -0.04 (0.51), residues: 115 loop : -0.61 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.011 0.001 PHE A 491 TYR 0.016 0.001 TYR A 362 ARG 0.005 0.000 ARG A 967 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2606.82 seconds wall clock time: 47 minutes 13.75 seconds (2833.75 seconds total)