Starting phenix.real_space_refine on Thu May 15 15:17:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6o_41073/05_2025/8t6o_41073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6o_41073/05_2025/8t6o_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/cci-nas-00/data/ceres_data/8t6o_41073/05_2025/8t6o_41073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6o_41073/05_2025/8t6o_41073.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6o_41073/05_2025/8t6o_41073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6o_41073/05_2025/8t6o_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. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.68, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.2 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: 4.19 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: 5.55 Time building geometry restraints manager: 3.42 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: 0.00 - 14.37: 17320 14.37 - 28.74: 3 28.74 - 43.11: 1 43.11 - 57.48: 0 57.48 - 71.85: 1 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 3.040 nonbonded pdb=" O LEU A1266 " pdb=" OH TYR A1294 " model vdw 2.229 3.040 nonbonded pdb=" O TYR A1237 " pdb=" OG SER A1240 " model vdw 2.301 3.040 nonbonded pdb=" O LEU A1291 " pdb=" ND2 ASN A1295 " model vdw 2.313 3.120 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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- 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= 0.308 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 Details of bonding type rmsd hydrogen bonds : bond 0.16116 ( 554) hydrogen bonds : angle 7.06848 ( 1509) covalent geometry : bond 0.00927 (12399) covalent geometry : angle 1.23037 (17325) *********************** 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 to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.152 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: 0.2321 time to fit residues: 45.1632 Evaluate side-chains 104 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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: 10.0000 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.106441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073512 restraints weight = 33813.744| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.27 r_work: 0.3166 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12399 Z= 0.255 Angle : 0.707 8.560 17325 Z= 0.380 Chirality : 0.042 0.214 2009 Planarity : 0.005 0.084 1736 Dihedral : 20.942 140.611 3042 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.24 % Allowed : 11.70 % Favored : 86.06 % 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: -0.30 (0.24), residues: 1129 helix: 0.24 (0.21), residues: 583 sheet: -0.46 (0.44), residues: 118 loop : -0.55 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 464 HIS 0.008 0.001 HIS A 129 PHE 0.019 0.002 PHE A1313 TYR 0.020 0.002 TYR A 362 ARG 0.004 0.001 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 554) hydrogen bonds : angle 5.34996 ( 1509) covalent geometry : bond 0.00548 (12399) covalent geometry : angle 0.70683 (17325) *********************** 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 125 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8814 (tp30) cc_final: 0.8581 (tp30) REVERT: A 251 ASN cc_start: 0.9222 (m-40) cc_final: 0.8307 (m-40) REVERT: A 263 LYS cc_start: 0.9450 (tttp) cc_final: 0.9058 (mmtt) REVERT: A 465 MET cc_start: 0.9031 (ppp) cc_final: 0.8818 (ppp) REVERT: A 560 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.6708 (t) REVERT: A 631 MET cc_start: 0.8713 (tpp) cc_final: 0.8492 (tpp) REVERT: A 670 ILE cc_start: 0.8076 (mm) cc_final: 0.7856 (mp) REVERT: A 763 MET cc_start: 0.9022 (tpp) cc_final: 0.8386 (mtp) REVERT: A 1043 MET cc_start: 0.7975 (pmm) cc_final: 0.6782 (tmm) REVERT: A 1125 ASP cc_start: 0.8918 (t0) cc_final: 0.8677 (t0) REVERT: A 1180 ASP cc_start: 0.9146 (t0) cc_final: 0.8939 (t0) outliers start: 22 outliers final: 9 residues processed: 117 average time/residue: 0.2120 time to fit residues: 37.5213 Evaluate side-chains 101 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 SER 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 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 101 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 726 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.108237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074822 restraints weight = 34189.103| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.30 r_work: 0.3227 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2521 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= 0.131 Angle : 0.573 9.979 17325 Z= 0.310 Chirality : 0.038 0.198 2009 Planarity : 0.004 0.055 1736 Dihedral : 20.870 142.426 3042 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.93 % Allowed : 12.51 % Favored : 85.55 % 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: 0.17 (0.24), residues: 1129 helix: 0.76 (0.22), residues: 589 sheet: -0.38 (0.45), residues: 118 loop : -0.51 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.004 0.001 HIS A 129 PHE 0.011 0.001 PHE A 491 TYR 0.014 0.001 TYR A 362 ARG 0.005 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 554) hydrogen bonds : angle 4.85630 ( 1509) covalent geometry : bond 0.00284 (12399) covalent geometry : angle 0.57268 (17325) *********************** 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 126 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8675 (tp30) cc_final: 0.8365 (tp30) REVERT: A 251 ASN cc_start: 0.9224 (m-40) cc_final: 0.8174 (m-40) REVERT: A 261 ASP cc_start: 0.8582 (m-30) cc_final: 0.8350 (m-30) REVERT: A 263 LYS cc_start: 0.9495 (tttp) cc_final: 0.9127 (mmtt) REVERT: A 631 MET cc_start: 0.8835 (tpp) cc_final: 0.8556 (tpp) REVERT: A 746 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 762 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 930 HIS cc_start: 0.8592 (m90) cc_final: 0.8364 (m90) REVERT: A 1043 MET cc_start: 0.8059 (pmm) cc_final: 0.6867 (tmm) REVERT: A 1125 ASP cc_start: 0.8850 (t0) cc_final: 0.8580 (t0) REVERT: A 1180 ASP cc_start: 0.9045 (t0) cc_final: 0.8831 (t0) REVERT: A 1189 GLU cc_start: 0.9027 (tp30) cc_final: 0.8677 (tp30) outliers start: 19 outliers final: 7 residues processed: 120 average time/residue: 0.2388 time to fit residues: 42.8375 Evaluate side-chains 103 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1305 GLN Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 65 optimal weight: 0.0010 chunk 116 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.108209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075020 restraints weight = 33723.876| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.27 r_work: 0.3229 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2878 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= 0.124 Angle : 0.560 8.410 17325 Z= 0.296 Chirality : 0.037 0.209 2009 Planarity : 0.003 0.049 1736 Dihedral : 20.732 145.090 3042 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 13.22 % 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: 0.46 (0.25), residues: 1129 helix: 1.03 (0.22), residues: 590 sheet: -0.31 (0.46), residues: 117 loop : -0.43 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 723 PHE 0.011 0.001 PHE A 966 TYR 0.018 0.001 TYR A 362 ARG 0.005 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 554) hydrogen bonds : angle 4.68468 ( 1509) covalent geometry : bond 0.00264 (12399) covalent geometry : angle 0.55970 (17325) *********************** 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 118 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8601 (tp30) cc_final: 0.8251 (tp30) REVERT: A 251 ASN cc_start: 0.9174 (m-40) cc_final: 0.7105 (m-40) REVERT: A 261 ASP cc_start: 0.8519 (m-30) cc_final: 0.7741 (t0) REVERT: A 263 LYS cc_start: 0.9490 (tttp) cc_final: 0.8843 (mmtt) REVERT: A 327 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: A 397 ASP cc_start: 0.8162 (t0) cc_final: 0.7489 (t0) REVERT: A 631 MET cc_start: 0.8842 (tpp) cc_final: 0.8572 (tpp) REVERT: A 746 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: A 762 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 763 MET cc_start: 0.8906 (tpp) cc_final: 0.8681 (ttt) REVERT: A 930 HIS cc_start: 0.8587 (m90) cc_final: 0.8318 (m90) REVERT: A 1043 MET cc_start: 0.8087 (pmm) cc_final: 0.6940 (tmm) REVERT: A 1125 ASP cc_start: 0.8883 (t0) cc_final: 0.8618 (t0) REVERT: A 1180 ASP cc_start: 0.9022 (t0) cc_final: 0.8798 (t0) REVERT: A 1189 GLU cc_start: 0.9029 (tp30) cc_final: 0.8678 (tp30) REVERT: A 1352 ILE cc_start: 0.9275 (tp) cc_final: 0.9068 (tp) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.2452 time to fit residues: 42.6948 Evaluate side-chains 98 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 213 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.107506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074611 restraints weight = 33820.596| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.23 r_work: 0.3225 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12399 Z= 0.132 Angle : 0.543 9.617 17325 Z= 0.290 Chirality : 0.037 0.188 2009 Planarity : 0.003 0.049 1736 Dihedral : 20.653 146.450 3042 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 12.72 % Favored : 85.15 % 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: 0.64 (0.25), residues: 1129 helix: 1.16 (0.22), residues: 591 sheet: -0.06 (0.47), residues: 110 loop : -0.38 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 PHE 0.012 0.001 PHE A1324 TYR 0.018 0.001 TYR A 362 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 554) hydrogen bonds : angle 4.58445 ( 1509) covalent geometry : bond 0.00285 (12399) covalent geometry : angle 0.54277 (17325) *********************** 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 113 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8601 (tp30) cc_final: 0.8235 (tp30) REVERT: A 251 ASN cc_start: 0.9089 (m-40) cc_final: 0.7463 (m-40) REVERT: A 261 ASP cc_start: 0.8455 (m-30) cc_final: 0.7788 (t0) REVERT: A 263 LYS cc_start: 0.9472 (tttp) cc_final: 0.8778 (tppt) REVERT: A 304 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8537 (m-30) REVERT: A 327 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 397 ASP cc_start: 0.8099 (t0) cc_final: 0.7372 (t0) REVERT: A 631 MET cc_start: 0.8867 (tpp) cc_final: 0.8545 (tpp) REVERT: A 634 GLU cc_start: 0.9261 (tp30) cc_final: 0.8945 (tm-30) REVERT: A 746 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: A 762 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7061 (tm-30) REVERT: A 930 HIS cc_start: 0.8611 (m90) cc_final: 0.8377 (m90) REVERT: A 1043 MET cc_start: 0.8112 (pmm) cc_final: 0.7019 (tmm) REVERT: A 1125 ASP cc_start: 0.8887 (t0) cc_final: 0.8623 (t0) REVERT: A 1180 ASP cc_start: 0.9031 (t0) cc_final: 0.8813 (t0) REVERT: A 1189 GLU cc_start: 0.9052 (tp30) cc_final: 0.8706 (tp30) REVERT: A 1241 HIS cc_start: 0.8409 (m90) cc_final: 0.8116 (m-70) REVERT: A 1352 ILE cc_start: 0.9330 (tp) cc_final: 0.9029 (tp) outliers start: 21 outliers final: 10 residues processed: 106 average time/residue: 0.2088 time to fit residues: 33.7127 Evaluate side-chains 99 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 213 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.105548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.072333 restraints weight = 34441.777| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.26 r_work: 0.3181 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12399 Z= 0.171 Angle : 0.565 8.885 17325 Z= 0.300 Chirality : 0.038 0.193 2009 Planarity : 0.003 0.050 1736 Dihedral : 20.637 146.686 3042 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.34 % Allowed : 13.33 % Favored : 84.33 % 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: 0.68 (0.25), residues: 1129 helix: 1.27 (0.22), residues: 585 sheet: -0.25 (0.47), residues: 115 loop : -0.38 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE A 966 TYR 0.019 0.001 TYR A 362 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 554) hydrogen bonds : angle 4.64225 ( 1509) covalent geometry : bond 0.00366 (12399) covalent geometry : angle 0.56503 (17325) *********************** 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 to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8700 (tp30) cc_final: 0.8339 (tp30) REVERT: A 110 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7632 (p0) REVERT: A 251 ASN cc_start: 0.9070 (m-40) cc_final: 0.7444 (m-40) REVERT: A 261 ASP cc_start: 0.8443 (m-30) cc_final: 0.7788 (t0) REVERT: A 263 LYS cc_start: 0.9466 (tttp) cc_final: 0.8785 (tppt) REVERT: A 304 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: A 327 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: A 397 ASP cc_start: 0.8167 (t0) cc_final: 0.7422 (t0) REVERT: A 631 MET cc_start: 0.8893 (tpp) cc_final: 0.8534 (tpp) REVERT: A 634 GLU cc_start: 0.9257 (tp30) cc_final: 0.8941 (tm-30) REVERT: A 746 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: A 762 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7031 (tm-30) REVERT: A 930 HIS cc_start: 0.8679 (m90) cc_final: 0.8408 (m90) REVERT: A 1043 MET cc_start: 0.8039 (pmm) cc_final: 0.6747 (tmm) REVERT: A 1125 ASP cc_start: 0.8952 (t0) cc_final: 0.8640 (t0) REVERT: A 1180 ASP cc_start: 0.9072 (t0) cc_final: 0.8858 (t0) REVERT: A 1189 GLU cc_start: 0.9081 (tp30) cc_final: 0.8758 (tp30) REVERT: A 1352 ILE cc_start: 0.9321 (tp) cc_final: 0.8991 (tp) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 0.2017 time to fit residues: 33.8369 Evaluate side-chains 104 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 404 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A1241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.107219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074368 restraints weight = 34299.531| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.23 r_work: 0.3213 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12399 Z= 0.127 Angle : 0.539 9.780 17325 Z= 0.283 Chirality : 0.037 0.186 2009 Planarity : 0.003 0.052 1736 Dihedral : 20.603 147.500 3042 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Rotamer: Outliers : 2.34 % Allowed : 13.53 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1129 helix: 1.35 (0.22), residues: 591 sheet: 0.01 (0.48), residues: 110 loop : -0.45 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 PHE 0.012 0.001 PHE A 966 TYR 0.016 0.001 TYR A1201 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 554) hydrogen bonds : angle 4.53577 ( 1509) covalent geometry : bond 0.00274 (12399) covalent geometry : angle 0.53943 (17325) *********************** 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 120 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8661 (tp30) cc_final: 0.8279 (tp30) REVERT: A 251 ASN cc_start: 0.9056 (m-40) cc_final: 0.8796 (m-40) REVERT: A 304 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: A 327 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: A 397 ASP cc_start: 0.8148 (t0) cc_final: 0.7386 (t70) REVERT: A 631 MET cc_start: 0.8812 (tpp) cc_final: 0.8429 (tpp) REVERT: A 634 GLU cc_start: 0.9254 (tp30) cc_final: 0.8914 (tm-30) REVERT: A 746 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: A 762 GLU cc_start: 0.7806 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 1043 MET cc_start: 0.8142 (pmm) cc_final: 0.6910 (tmm) REVERT: A 1125 ASP cc_start: 0.8883 (t0) cc_final: 0.8574 (t0) REVERT: A 1180 ASP cc_start: 0.9051 (t0) cc_final: 0.8842 (t0) REVERT: A 1189 GLU cc_start: 0.9118 (tp30) cc_final: 0.8833 (tp30) REVERT: A 1241 HIS cc_start: 0.8402 (m170) cc_final: 0.8178 (m-70) REVERT: A 1352 ILE cc_start: 0.9308 (tp) cc_final: 0.8958 (tp) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 0.2359 time to fit residues: 39.8551 Evaluate side-chains 104 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.3980 chunk 71 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.107640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074960 restraints weight = 34550.887| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.23 r_work: 0.3221 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4043 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= 0.120 Angle : 0.534 9.480 17325 Z= 0.280 Chirality : 0.036 0.170 2009 Planarity : 0.003 0.044 1736 Dihedral : 20.533 150.855 3042 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 2.03 % Allowed : 14.04 % Favored : 83.93 % 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: 0.83 (0.25), residues: 1129 helix: 1.40 (0.22), residues: 591 sheet: -0.14 (0.48), residues: 117 loop : -0.38 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A 723 PHE 0.021 0.001 PHE A1258 TYR 0.016 0.001 TYR A 362 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 554) hydrogen bonds : angle 4.50659 ( 1509) covalent geometry : bond 0.00257 (12399) covalent geometry : angle 0.53404 (17325) *********************** 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 117 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8632 (tp30) cc_final: 0.8251 (tp30) REVERT: A 110 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7612 (p0) REVERT: A 304 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: A 327 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 397 ASP cc_start: 0.8159 (t0) cc_final: 0.7399 (t0) REVERT: A 631 MET cc_start: 0.8844 (tpp) cc_final: 0.8467 (tpp) REVERT: A 634 GLU cc_start: 0.9256 (tp30) cc_final: 0.8923 (tm-30) REVERT: A 746 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 762 GLU cc_start: 0.7820 (tm-30) cc_final: 0.6863 (tm-30) REVERT: A 959 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7644 (ptpt) REVERT: A 1043 MET cc_start: 0.8129 (pmm) cc_final: 0.6911 (tmm) REVERT: A 1125 ASP cc_start: 0.8863 (t0) cc_final: 0.8543 (t0) REVERT: A 1180 ASP cc_start: 0.9036 (t0) cc_final: 0.8823 (t0) REVERT: A 1189 GLU cc_start: 0.9114 (tp30) cc_final: 0.8847 (tp30) REVERT: A 1241 HIS cc_start: 0.8413 (m170) cc_final: 0.8144 (m-70) REVERT: A 1352 ILE cc_start: 0.9300 (tp) cc_final: 0.8940 (tp) outliers start: 20 outliers final: 12 residues processed: 113 average time/residue: 0.2206 time to fit residues: 37.9887 Evaluate side-chains 104 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 590 SER Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 720 LEU 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 1305 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 98 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 102 optimal weight: 0.0070 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN A 940 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.107081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074132 restraints weight = 33923.687| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.23 r_work: 0.3229 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12399 Z= 0.115 Angle : 0.545 10.273 17325 Z= 0.285 Chirality : 0.037 0.240 2009 Planarity : 0.003 0.046 1736 Dihedral : 20.494 153.087 3042 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 1.83 % Allowed : 15.16 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.25), residues: 1129 helix: 1.36 (0.22), residues: 591 sheet: 0.11 (0.50), residues: 110 loop : -0.36 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 723 PHE 0.024 0.001 PHE A1258 TYR 0.017 0.001 TYR A1201 ARG 0.004 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 554) hydrogen bonds : angle 4.55533 ( 1509) covalent geometry : bond 0.00247 (12399) covalent geometry : angle 0.54459 (17325) *********************** 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 109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8629 (tp30) cc_final: 0.8204 (tp30) REVERT: A 304 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: A 397 ASP cc_start: 0.8195 (t0) cc_final: 0.7531 (t0) REVERT: A 631 MET cc_start: 0.8833 (tpp) cc_final: 0.8442 (tpp) REVERT: A 634 GLU cc_start: 0.9251 (tp30) cc_final: 0.8914 (tm-30) REVERT: A 746 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 959 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7607 (ptpt) REVERT: A 1043 MET cc_start: 0.8115 (pmm) cc_final: 0.6908 (tmm) REVERT: A 1125 ASP cc_start: 0.8843 (t0) cc_final: 0.8546 (t0) REVERT: A 1180 ASP cc_start: 0.9041 (t0) cc_final: 0.8828 (t0) REVERT: A 1189 GLU cc_start: 0.9135 (tp30) cc_final: 0.8881 (tp30) REVERT: A 1241 HIS cc_start: 0.8431 (m170) cc_final: 0.8146 (m-70) REVERT: A 1352 ILE cc_start: 0.9298 (tp) cc_final: 0.8933 (tp) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 0.1994 time to fit residues: 32.1796 Evaluate side-chains 103 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 213 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 404 THR 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 720 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 997 LEU 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 104 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.102458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069347 restraints weight = 34776.487| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.31 r_work: 0.3084 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12399 Z= 0.345 Angle : 0.737 10.401 17325 Z= 0.382 Chirality : 0.044 0.275 2009 Planarity : 0.004 0.047 1736 Dihedral : 20.775 149.998 3042 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 2.03 % Allowed : 15.67 % Favored : 82.30 % 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: 0.25 (0.24), residues: 1129 helix: 0.97 (0.21), residues: 589 sheet: -0.27 (0.48), residues: 114 loop : -0.76 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 464 HIS 0.011 0.002 HIS A 328 PHE 0.025 0.002 PHE A1258 TYR 0.024 0.002 TYR A 362 ARG 0.006 0.001 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 554) hydrogen bonds : angle 5.11272 ( 1509) covalent geometry : bond 0.00738 (12399) covalent geometry : angle 0.73679 (17325) ********************** 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 107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8872 (tp30) cc_final: 0.8515 (tp30) REVERT: A 304 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8695 (m-30) REVERT: A 634 GLU cc_start: 0.9223 (tp30) cc_final: 0.8902 (tm-30) REVERT: A 959 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7920 (pttt) REVERT: A 1043 MET cc_start: 0.8079 (pmm) cc_final: 0.6886 (tmm) REVERT: A 1189 GLU cc_start: 0.9244 (tp30) cc_final: 0.8976 (tp30) REVERT: A 1241 HIS cc_start: 0.8519 (m170) cc_final: 0.8221 (m-70) REVERT: A 1352 ILE cc_start: 0.9378 (tp) cc_final: 0.9034 (tp) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 0.2281 time to fit residues: 35.0333 Evaluate side-chains 98 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 304 ASP 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 616 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 997 LEU 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 86 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.108216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076451 restraints weight = 33451.532| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.34 r_work: 0.3195 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12399 Z= 0.121 Angle : 0.585 10.976 17325 Z= 0.304 Chirality : 0.038 0.256 2009 Planarity : 0.003 0.042 1736 Dihedral : 20.698 151.642 3042 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.42 % Allowed : 16.17 % Favored : 82.40 % 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: 1.28 (0.22), residues: 584 sheet: -0.12 (0.58), residues: 87 loop : -0.47 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 PHE 0.020 0.001 PHE A1258 TYR 0.014 0.001 TYR A 362 ARG 0.008 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 554) hydrogen bonds : angle 4.72787 ( 1509) covalent geometry : bond 0.00259 (12399) covalent geometry : angle 0.58528 (17325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6779.68 seconds wall clock time: 118 minutes 2.34 seconds (7082.34 seconds total)