Starting phenix.real_space_refine on Wed Mar 12 18:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0g_42854/03_2025/8v0g_42854_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0g_42854/03_2025/8v0g_42854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0g_42854/03_2025/8v0g_42854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0g_42854/03_2025/8v0g_42854.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0g_42854/03_2025/8v0g_42854_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0g_42854/03_2025/8v0g_42854_neut.cif" } resolution = 3.11 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= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5328 2.51 5 N 1268 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8106 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 8050 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS%COO:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.52, per 1000 atoms: 0.68 Number of scatterers: 8106 At special positions: 0 Unit cell: (89.88, 98.44, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1465 8.00 N 1268 7.00 C 5328 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 Links applied NAG-ASN " NAG A1502 " - " ASN A 165 " " NAG A1503 " - " ASN A 294 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 961.7 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 8 sheets defined 71.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 35 removed outlier: 3.543A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.610A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 103 through 120 removed outlier: 3.609A pdb=" N THR A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 141 through 162 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.582A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.714A pdb=" N CYS A 353 " --> pdb=" O GLU A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 435 through 453 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.569A pdb=" N ILE A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 493 through 516 Processing helix chain 'A' and resid 524 through 550 removed outlier: 3.679A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.573A pdb=" N ASP A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 619 removed outlier: 4.751A pdb=" N LEU A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 645 Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 663 through 673 Processing helix chain 'A' and resid 722 through 736 Processing helix chain 'A' and resid 1046 through 1050 Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1067 through 1074 Processing helix chain 'A' and resid 1074 through 1098 Processing helix chain 'A' and resid 1104 through 1109 Processing helix chain 'A' and resid 1113 through 1126 Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.653A pdb=" N GLU A1150 " --> pdb=" O TYR A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 removed outlier: 3.641A pdb=" N SER A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1201 Processing helix chain 'A' and resid 1209 through 1218 Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1226 through 1241 Processing helix chain 'A' and resid 1241 through 1247 Processing helix chain 'A' and resid 1272 through 1287 Processing helix chain 'A' and resid 1290 through 1293 Processing helix chain 'A' and resid 1301 through 1335 removed outlier: 4.486A pdb=" N PHE A1305 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A1309 " --> pdb=" O PHE A1305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A1313 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU A1314 " --> pdb=" O GLU A1310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1362 Processing helix chain 'A' and resid 1367 through 1395 removed outlier: 3.876A pdb=" N VAL A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY A1379 " --> pdb=" O VAL A1375 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A1380 " --> pdb=" O LEU A1376 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A1384 " --> pdb=" O PHE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1428 removed outlier: 5.698A pdb=" N GLY A1413 " --> pdb=" O HIS A1409 " (cutoff:3.500A) Proline residue: A1414 - end of helix removed outlier: 4.111A pdb=" N THR A1428 " --> pdb=" O PHE A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1432 Processing helix chain 'A' and resid 1434 through 1457 Processing helix chain 'A' and resid 1457 through 1467 Processing sheet with id=AA1, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.783A pdb=" N ALA A 422 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.460A pdb=" N LEU A1254 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS A1264 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A1207 " --> pdb=" O HIS A1264 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A1266 " --> pdb=" O THR A1205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.460A pdb=" N LEU A1254 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.789A pdb=" N ILE A 380 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 390 Processing sheet with id=AA8, first strand: chain 'A' and resid 1288 through 1289 533 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2437 1.34 - 1.45: 1741 1.45 - 1.57: 4052 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8298 Sorted by residual: bond pdb=" C PHE A1211 " pdb=" N THR A1212 " ideal model delta sigma weight residual 1.335 1.381 -0.047 1.25e-02 6.40e+03 1.40e+01 bond pdb=" C PHE A 733 " pdb=" N GLU A 734 " ideal model delta sigma weight residual 1.334 1.303 0.032 1.27e-02 6.20e+03 6.16e+00 bond pdb=" C PRO A 137 " pdb=" O PRO A 137 " ideal model delta sigma weight residual 1.246 1.229 0.017 8.50e-03 1.38e+04 3.93e+00 bond pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 1.524 1.504 0.021 1.05e-02 9.07e+03 3.83e+00 bond pdb=" CA PRO A 555 " pdb=" C PRO A 555 " ideal model delta sigma weight residual 1.517 1.534 -0.017 9.30e-03 1.16e+04 3.38e+00 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10139 1.53 - 3.06: 911 3.06 - 4.60: 131 4.60 - 6.13: 21 6.13 - 7.66: 6 Bond angle restraints: 11208 Sorted by residual: angle pdb=" CA VAL A1069 " pdb=" C VAL A1069 " pdb=" N PRO A1070 " ideal model delta sigma weight residual 120.83 117.37 3.46 6.10e-01 2.69e+00 3.22e+01 angle pdb=" CA VAL A 560 " pdb=" C VAL A 560 " pdb=" N PRO A 561 " ideal model delta sigma weight residual 120.83 117.57 3.26 6.10e-01 2.69e+00 2.86e+01 angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 111.71 105.77 5.94 1.15e+00 7.56e-01 2.67e+01 angle pdb=" N GLY A1102 " pdb=" CA GLY A1102 " pdb=" C GLY A1102 " ideal model delta sigma weight residual 112.18 118.49 -6.31 1.34e+00 5.57e-01 2.22e+01 angle pdb=" N LYS A1336 " pdb=" CA LYS A1336 " pdb=" C LYS A1336 " ideal model delta sigma weight residual 111.07 115.68 -4.61 1.07e+00 8.73e-01 1.86e+01 ... (remaining 11203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 4839 22.60 - 45.20: 129 45.20 - 67.80: 15 67.80 - 90.39: 6 90.39 - 112.99: 3 Dihedral angle restraints: 4992 sinusoidal: 2077 harmonic: 2915 Sorted by residual: dihedral pdb=" C1 NAG A1503 " pdb=" C5 NAG A1503 " pdb=" O5 NAG A1503 " pdb=" C6 NAG A1503 " ideal model delta sinusoidal sigma weight residual 171.16 -75.85 -112.99 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C1 NAG A1503 " pdb=" C5 NAG A1503 " pdb=" O5 NAG A1503 " pdb=" C4 NAG A1503 " ideal model delta sinusoidal sigma weight residual -64.11 47.95 -112.06 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C2 NAG A1503 " pdb=" C1 NAG A1503 " pdb=" O5 NAG A1503 " pdb=" C5 NAG A1503 " ideal model delta sinusoidal sigma weight residual -62.96 37.14 -100.10 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1123 0.069 - 0.139: 136 0.139 - 0.208: 3 0.208 - 0.277: 1 0.277 - 0.347: 2 Chirality restraints: 1265 Sorted by residual: chirality pdb=" C1 NAG A1503 " pdb=" ND2 ASN A 294 " pdb=" C2 NAG A1503 " pdb=" O5 NAG A1503 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C13 CLR A1501 " pdb=" C12 CLR A1501 " pdb=" C14 CLR A1501 " pdb=" C17 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C14 CLR A1501 " pdb=" C13 CLR A1501 " pdb=" C15 CLR A1501 " pdb=" C8 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1262 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1502 " 0.227 2.00e-02 2.50e+03 1.92e-01 4.62e+02 pdb=" C7 NAG A1502 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG A1502 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG A1502 " -0.314 2.00e-02 2.50e+03 pdb=" O7 NAG A1502 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1503 " -0.136 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" C7 NAG A1503 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A1503 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG A1503 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG A1503 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1459 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A1460 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1460 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1460 " 0.022 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 4580 2.91 - 3.41: 9629 3.41 - 3.91: 14674 3.91 - 4.40: 18127 4.40 - 4.90: 26123 Nonbonded interactions: 73133 Sorted by model distance: nonbonded pdb=" OH TYR A 86 " pdb=" O ILE A 309 " model vdw 2.417 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" OG SER A 125 " model vdw 2.429 3.040 nonbonded pdb=" O GLU A1150 " pdb=" C LYS A1151 " model vdw 2.429 3.270 nonbonded pdb=" O TYR A1059 " pdb=" OG SER A1062 " model vdw 2.436 3.040 nonbonded pdb=" OH TYR A1068 " pdb=" O SER A1456 " model vdw 2.438 3.040 ... (remaining 73128 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.250 Find NCS groups from input model: 0.230 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.006 0.047 8298 Z= 0.409 Angle : 0.950 7.659 11208 Z= 0.677 Chirality : 0.043 0.347 1265 Planarity : 0.007 0.192 1382 Dihedral : 10.812 112.992 3112 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 0.88 % Allowed : 6.08 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.87 (0.23), residues: 975 helix: -1.04 (0.18), residues: 629 sheet: -1.18 (0.68), residues: 51 loop : -1.30 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.010 0.001 PHE A 548 TYR 0.010 0.001 TYR A1136 ARG 0.003 0.000 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 294 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9341 (tt) cc_final: 0.9114 (tt) REVERT: A 352 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 1222 LEU cc_start: 0.8751 (mp) cc_final: 0.8509 (mp) outliers start: 8 outliers final: 3 residues processed: 298 average time/residue: 0.2043 time to fit residues: 82.1117 Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 431 ASN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN A1184 ASN A1201 GLN A1228 GLN A1255 ASN A1291 ASN A1293 ASN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076744 restraints weight = 17243.774| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.15 r_work: 0.2926 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8298 Z= 0.256 Angle : 0.670 9.816 11208 Z= 0.352 Chirality : 0.043 0.165 1265 Planarity : 0.005 0.045 1382 Dihedral : 7.453 97.674 1176 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.76 % Allowed : 13.37 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 975 helix: 1.57 (0.20), residues: 621 sheet: -0.53 (0.70), residues: 52 loop : -0.13 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 726 HIS 0.007 0.002 HIS A1417 PHE 0.023 0.002 PHE A 733 TYR 0.016 0.002 TYR A 304 ARG 0.004 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 152 ILE cc_start: 0.9364 (tp) cc_final: 0.9119 (pt) REVERT: A 336 GLU cc_start: 0.9105 (tp30) cc_final: 0.8602 (tt0) REVERT: A 360 CYS cc_start: 0.8962 (m) cc_final: 0.8468 (m) REVERT: A 543 SER cc_start: 0.9081 (m) cc_final: 0.8779 (p) REVERT: A 1055 ASN cc_start: 0.8296 (m-40) cc_final: 0.8036 (m-40) REVERT: A 1278 LYS cc_start: 0.9186 (tppp) cc_final: 0.8947 (tppp) REVERT: A 1352 ASP cc_start: 0.8802 (m-30) cc_final: 0.8586 (m-30) REVERT: A 1398 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8156 (mtm180) outliers start: 25 outliers final: 9 residues processed: 206 average time/residue: 0.1550 time to fit residues: 46.9125 Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 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 8 HIS ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 ASN ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1394 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072908 restraints weight = 17899.983| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.32 r_work: 0.2906 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8298 Z= 0.226 Angle : 0.584 9.422 11208 Z= 0.308 Chirality : 0.042 0.201 1265 Planarity : 0.004 0.043 1382 Dihedral : 6.967 90.653 1170 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.09 % Allowed : 14.92 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.06 (0.27), residues: 975 helix: 2.11 (0.20), residues: 617 sheet: -0.47 (0.67), residues: 52 loop : 0.25 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.005 0.001 HIS A1195 PHE 0.017 0.002 PHE A 733 TYR 0.015 0.001 TYR A 304 ARG 0.003 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.990 Fit side-chains REVERT: A 19 ASP cc_start: 0.9285 (m-30) cc_final: 0.8824 (m-30) REVERT: A 52 CYS cc_start: 0.8955 (m) cc_final: 0.8468 (t) REVERT: A 145 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8693 (mppt) REVERT: A 146 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8821 (mm-30) REVERT: A 156 GLU cc_start: 0.9158 (tp30) cc_final: 0.8896 (tp30) REVERT: A 160 LYS cc_start: 0.9555 (ttmm) cc_final: 0.9350 (ttmm) REVERT: A 336 GLU cc_start: 0.9074 (tp30) cc_final: 0.8599 (tt0) REVERT: A 493 ASP cc_start: 0.8055 (t0) cc_final: 0.7472 (t0) REVERT: A 543 SER cc_start: 0.9075 (m) cc_final: 0.8774 (p) REVERT: A 598 ASP cc_start: 0.8927 (m-30) cc_final: 0.8693 (m-30) REVERT: A 1055 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: A 1206 SER cc_start: 0.9087 (t) cc_final: 0.8879 (m) REVERT: A 1278 LYS cc_start: 0.9167 (tppp) cc_final: 0.8836 (tppp) REVERT: A 1352 ASP cc_start: 0.8911 (m-30) cc_final: 0.8639 (m-30) REVERT: A 1398 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8205 (mtm180) REVERT: A 1443 THR cc_start: 0.9694 (m) cc_final: 0.9406 (p) REVERT: A 1444 LEU cc_start: 0.9032 (tp) cc_final: 0.8746 (tp) outliers start: 28 outliers final: 14 residues processed: 186 average time/residue: 0.1677 time to fit residues: 44.8886 Evaluate side-chains 164 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 1055 ASN Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 chunk 62 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 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 = 0.3319 r_free = 0.3319 target = 0.089910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073931 restraints weight = 17696.898| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.23 r_work: 0.2901 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8298 Z= 0.212 Angle : 0.566 10.200 11208 Z= 0.297 Chirality : 0.041 0.185 1265 Planarity : 0.004 0.039 1382 Dihedral : 6.565 81.611 1170 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.87 % Allowed : 15.91 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.17 (0.27), residues: 975 helix: 2.19 (0.20), residues: 618 sheet: -0.32 (0.65), residues: 52 loop : 0.29 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1261 HIS 0.005 0.001 HIS A1195 PHE 0.021 0.001 PHE A 508 TYR 0.013 0.001 TYR A 304 ARG 0.004 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.972 Fit side-chains REVERT: A 19 ASP cc_start: 0.9294 (m-30) cc_final: 0.8768 (m-30) REVERT: A 52 CYS cc_start: 0.8907 (m) cc_final: 0.8438 (t) REVERT: A 142 HIS cc_start: 0.8391 (t-170) cc_final: 0.7980 (t-170) REVERT: A 145 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8658 (mppt) REVERT: A 146 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8711 (mm-30) REVERT: A 336 GLU cc_start: 0.9087 (tp30) cc_final: 0.8720 (pt0) REVERT: A 355 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8604 (mtpp) REVERT: A 360 CYS cc_start: 0.8185 (m) cc_final: 0.7863 (p) REVERT: A 543 SER cc_start: 0.9108 (m) cc_final: 0.8796 (p) REVERT: A 594 MET cc_start: 0.8840 (mtp) cc_final: 0.8416 (mtp) REVERT: A 598 ASP cc_start: 0.8938 (m-30) cc_final: 0.8706 (m-30) REVERT: A 721 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 1278 LYS cc_start: 0.9171 (tppp) cc_final: 0.8805 (tppp) REVERT: A 1398 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8216 (mtm180) REVERT: A 1444 LEU cc_start: 0.9088 (tp) cc_final: 0.8851 (tp) outliers start: 35 outliers final: 16 residues processed: 180 average time/residue: 0.1748 time to fit residues: 46.3066 Evaluate side-chains 162 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 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 = 0.3340 r_free = 0.3340 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075245 restraints weight = 17567.359| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.17 r_work: 0.2902 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8298 Z= 0.214 Angle : 0.567 10.970 11208 Z= 0.297 Chirality : 0.040 0.156 1265 Planarity : 0.004 0.038 1382 Dihedral : 6.009 68.313 1170 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.65 % Allowed : 15.91 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.22 (0.27), residues: 975 helix: 2.22 (0.20), residues: 618 sheet: -0.21 (0.65), residues: 52 loop : 0.31 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.020 0.002 PHE A 6 TYR 0.012 0.001 TYR A 304 ARG 0.004 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9287 (m-30) cc_final: 0.8882 (m-30) REVERT: A 52 CYS cc_start: 0.8809 (m) cc_final: 0.8435 (t) REVERT: A 67 TYR cc_start: 0.9157 (m-80) cc_final: 0.8839 (m-80) REVERT: A 142 HIS cc_start: 0.8344 (t-170) cc_final: 0.7839 (t-170) REVERT: A 145 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8876 (tppt) REVERT: A 146 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8723 (mm-30) REVERT: A 156 GLU cc_start: 0.9122 (tp30) cc_final: 0.8862 (tp30) REVERT: A 160 LYS cc_start: 0.9575 (ttmm) cc_final: 0.9356 (ttmm) REVERT: A 336 GLU cc_start: 0.9078 (tp30) cc_final: 0.8667 (pt0) REVERT: A 360 CYS cc_start: 0.8274 (m) cc_final: 0.7761 (p) REVERT: A 543 SER cc_start: 0.9062 (m) cc_final: 0.8769 (p) REVERT: A 721 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 1278 LYS cc_start: 0.9185 (tppp) cc_final: 0.8803 (tppp) REVERT: A 1398 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8179 (mtm180) REVERT: A 1443 THR cc_start: 0.9702 (m) cc_final: 0.9440 (p) REVERT: A 1444 LEU cc_start: 0.9052 (tp) cc_final: 0.8801 (tp) outliers start: 33 outliers final: 19 residues processed: 182 average time/residue: 0.1660 time to fit residues: 44.0072 Evaluate side-chains 164 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 ASN Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** A1306 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 = 0.3293 r_free = 0.3293 target = 0.089492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.072732 restraints weight = 17628.277| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.35 r_work: 0.2900 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8298 Z= 0.202 Angle : 0.588 11.015 11208 Z= 0.302 Chirality : 0.040 0.184 1265 Planarity : 0.004 0.037 1382 Dihedral : 5.253 61.511 1170 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.09 % Allowed : 17.57 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.20 (0.27), residues: 975 helix: 2.19 (0.21), residues: 620 sheet: -0.21 (0.65), residues: 52 loop : 0.30 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.026 0.001 PHE A 733 TYR 0.018 0.001 TYR A 55 ARG 0.006 0.000 ARG A1223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9286 (m-30) cc_final: 0.8954 (m-30) REVERT: A 52 CYS cc_start: 0.8789 (m) cc_final: 0.8534 (t) REVERT: A 67 TYR cc_start: 0.9188 (m-80) cc_final: 0.8832 (m-80) REVERT: A 68 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8616 (p) REVERT: A 142 HIS cc_start: 0.8303 (t-170) cc_final: 0.7863 (t-170) REVERT: A 145 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8749 (mmtm) REVERT: A 146 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 336 GLU cc_start: 0.9093 (tp30) cc_final: 0.8666 (pt0) REVERT: A 360 CYS cc_start: 0.8311 (m) cc_final: 0.7711 (p) REVERT: A 493 ASP cc_start: 0.8187 (t0) cc_final: 0.7684 (t0) REVERT: A 543 SER cc_start: 0.9118 (m) cc_final: 0.8782 (p) REVERT: A 721 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 1278 LYS cc_start: 0.9143 (tppp) cc_final: 0.8750 (tppp) REVERT: A 1398 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8230 (mtm180) REVERT: A 1444 LEU cc_start: 0.9073 (tp) cc_final: 0.8866 (tp) outliers start: 28 outliers final: 18 residues processed: 180 average time/residue: 0.1644 time to fit residues: 42.8841 Evaluate side-chains 171 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1209 ASN Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.071439 restraints weight = 17885.857| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.38 r_work: 0.2875 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8298 Z= 0.262 Angle : 0.581 10.608 11208 Z= 0.304 Chirality : 0.042 0.225 1265 Planarity : 0.004 0.036 1382 Dihedral : 4.616 57.898 1170 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.31 % Allowed : 18.56 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.20 (0.27), residues: 975 helix: 2.20 (0.21), residues: 621 sheet: -0.24 (0.66), residues: 52 loop : 0.30 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.021 0.001 PHE A 733 TYR 0.012 0.001 TYR A 623 ARG 0.004 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9255 (m-30) cc_final: 0.8733 (m-30) REVERT: A 52 CYS cc_start: 0.8840 (m) cc_final: 0.8533 (t) REVERT: A 67 TYR cc_start: 0.9258 (m-80) cc_final: 0.8945 (m-80) REVERT: A 68 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 111 GLN cc_start: 0.8683 (tt0) cc_final: 0.8457 (tm-30) REVERT: A 142 HIS cc_start: 0.8289 (t-170) cc_final: 0.7946 (t-170) REVERT: A 145 LYS cc_start: 0.9291 (mmmt) cc_final: 0.8908 (tppt) REVERT: A 146 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 336 GLU cc_start: 0.9104 (tp30) cc_final: 0.8668 (pt0) REVERT: A 360 CYS cc_start: 0.8439 (m) cc_final: 0.7898 (p) REVERT: A 367 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8734 (tt) REVERT: A 493 ASP cc_start: 0.8234 (t0) cc_final: 0.7743 (t0) REVERT: A 509 MET cc_start: 0.8700 (mmm) cc_final: 0.8374 (tmm) REVERT: A 543 SER cc_start: 0.9152 (m) cc_final: 0.8799 (p) REVERT: A 721 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 1278 LYS cc_start: 0.9145 (tppp) cc_final: 0.8757 (tppp) REVERT: A 1398 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8242 (mtm180) REVERT: A 1444 LEU cc_start: 0.9096 (tp) cc_final: 0.8862 (tp) outliers start: 30 outliers final: 17 residues processed: 178 average time/residue: 0.1786 time to fit residues: 45.6565 Evaluate side-chains 169 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 ASN Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073274 restraints weight = 17999.299| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.42 r_work: 0.2900 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8298 Z= 0.197 Angle : 0.566 9.852 11208 Z= 0.294 Chirality : 0.041 0.212 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.366 52.546 1170 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.87 % Allowed : 19.89 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.23 (0.27), residues: 975 helix: 2.19 (0.21), residues: 620 sheet: -0.22 (0.67), residues: 52 loop : 0.41 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.003 0.001 HIS A 142 PHE 0.033 0.002 PHE A 513 TYR 0.011 0.001 TYR A 26 ARG 0.004 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9256 (m-30) cc_final: 0.8751 (m-30) REVERT: A 52 CYS cc_start: 0.8825 (m) cc_final: 0.8552 (t) REVERT: A 67 TYR cc_start: 0.9254 (m-80) cc_final: 0.8916 (m-80) REVERT: A 68 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8680 (p) REVERT: A 111 GLN cc_start: 0.8693 (tt0) cc_final: 0.8449 (tm-30) REVERT: A 142 HIS cc_start: 0.8185 (t-170) cc_final: 0.7851 (t-170) REVERT: A 145 LYS cc_start: 0.9314 (mmmt) cc_final: 0.8928 (tppt) REVERT: A 146 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8666 (mm-30) REVERT: A 336 GLU cc_start: 0.9110 (tp30) cc_final: 0.8715 (pt0) REVERT: A 360 CYS cc_start: 0.8293 (m) cc_final: 0.7765 (p) REVERT: A 493 ASP cc_start: 0.8269 (t0) cc_final: 0.7801 (t0) REVERT: A 509 MET cc_start: 0.8621 (mmm) cc_final: 0.8358 (tmm) REVERT: A 543 SER cc_start: 0.9120 (m) cc_final: 0.8766 (p) REVERT: A 658 GLU cc_start: 0.9073 (tt0) cc_final: 0.8713 (tp30) REVERT: A 721 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 1278 LYS cc_start: 0.9131 (tppp) cc_final: 0.8716 (tppp) REVERT: A 1352 ASP cc_start: 0.9034 (m-30) cc_final: 0.8758 (m-30) REVERT: A 1398 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8251 (mtm180) outliers start: 26 outliers final: 17 residues processed: 186 average time/residue: 0.1868 time to fit residues: 50.2114 Evaluate side-chains 180 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 ASN Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072760 restraints weight = 18159.335| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.42 r_work: 0.2897 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8298 Z= 0.217 Angle : 0.583 9.774 11208 Z= 0.304 Chirality : 0.041 0.203 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.270 49.096 1170 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.43 % Allowed : 19.89 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.21 (0.27), residues: 975 helix: 2.13 (0.21), residues: 626 sheet: -0.12 (0.68), residues: 52 loop : 0.43 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.033 0.002 PHE A 513 TYR 0.011 0.001 TYR A 623 ARG 0.005 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9251 (m-30) cc_final: 0.8745 (m-30) REVERT: A 52 CYS cc_start: 0.8827 (m) cc_final: 0.8550 (t) REVERT: A 67 TYR cc_start: 0.9278 (m-80) cc_final: 0.8925 (m-80) REVERT: A 68 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8676 (p) REVERT: A 111 GLN cc_start: 0.8695 (tt0) cc_final: 0.8446 (tm-30) REVERT: A 142 HIS cc_start: 0.8151 (t-170) cc_final: 0.7804 (t-170) REVERT: A 145 LYS cc_start: 0.9316 (mmmt) cc_final: 0.8949 (tppt) REVERT: A 146 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8641 (mm-30) REVERT: A 336 GLU cc_start: 0.9091 (tp30) cc_final: 0.8814 (pt0) REVERT: A 360 CYS cc_start: 0.8312 (m) cc_final: 0.7801 (p) REVERT: A 493 ASP cc_start: 0.8256 (t0) cc_final: 0.7896 (t0) REVERT: A 509 MET cc_start: 0.8696 (mmm) cc_final: 0.8372 (tmm) REVERT: A 543 SER cc_start: 0.9117 (m) cc_final: 0.8761 (p) REVERT: A 658 GLU cc_start: 0.9072 (tt0) cc_final: 0.8721 (tp30) REVERT: A 721 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 1278 LYS cc_start: 0.9135 (tppp) cc_final: 0.8716 (tppp) REVERT: A 1352 ASP cc_start: 0.9053 (m-30) cc_final: 0.8782 (m-30) REVERT: A 1371 MET cc_start: 0.9018 (mmp) cc_final: 0.8740 (mmm) outliers start: 22 outliers final: 17 residues processed: 179 average time/residue: 0.1684 time to fit residues: 43.4820 Evaluate side-chains 172 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 ASN Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072924 restraints weight = 18275.101| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.33 r_work: 0.2929 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8298 Z= 0.205 Angle : 0.599 9.735 11208 Z= 0.311 Chirality : 0.041 0.204 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.254 46.661 1170 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.65 % Allowed : 20.66 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.19 (0.27), residues: 975 helix: 2.07 (0.21), residues: 627 sheet: -0.05 (0.69), residues: 52 loop : 0.51 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.032 0.001 PHE A 513 TYR 0.010 0.001 TYR A 304 ARG 0.005 0.000 ARG A1147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9204 (m-30) cc_final: 0.8696 (m-30) REVERT: A 52 CYS cc_start: 0.8837 (m) cc_final: 0.8557 (t) REVERT: A 67 TYR cc_start: 0.9296 (m-80) cc_final: 0.9002 (m-80) REVERT: A 68 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 111 GLN cc_start: 0.8736 (tt0) cc_final: 0.8475 (tm-30) REVERT: A 142 HIS cc_start: 0.8080 (t-170) cc_final: 0.7818 (t-170) REVERT: A 145 LYS cc_start: 0.9342 (mmmt) cc_final: 0.8893 (tppt) REVERT: A 146 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 336 GLU cc_start: 0.9084 (tp30) cc_final: 0.8851 (pt0) REVERT: A 360 CYS cc_start: 0.8213 (m) cc_final: 0.7721 (p) REVERT: A 457 ASP cc_start: 0.9104 (p0) cc_final: 0.8644 (m-30) REVERT: A 460 GLN cc_start: 0.7889 (mt0) cc_final: 0.7492 (mp10) REVERT: A 493 ASP cc_start: 0.8289 (t0) cc_final: 0.7889 (t0) REVERT: A 508 PHE cc_start: 0.9137 (t80) cc_final: 0.8766 (t80) REVERT: A 509 MET cc_start: 0.8707 (mmm) cc_final: 0.8425 (tmm) REVERT: A 543 SER cc_start: 0.9133 (m) cc_final: 0.8787 (p) REVERT: A 658 GLU cc_start: 0.9028 (tt0) cc_final: 0.8703 (tp30) REVERT: A 721 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (tp) REVERT: A 1278 LYS cc_start: 0.9128 (tppp) cc_final: 0.8705 (tppp) REVERT: A 1398 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8296 (mtm180) outliers start: 24 outliers final: 19 residues processed: 177 average time/residue: 0.2289 time to fit residues: 59.5942 Evaluate side-chains 178 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 ASN Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073985 restraints weight = 18311.177| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.31 r_work: 0.2949 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8298 Z= 0.187 Angle : 0.583 9.717 11208 Z= 0.302 Chirality : 0.041 0.205 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.181 43.138 1170 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.54 % Allowed : 20.88 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.26 (0.27), residues: 975 helix: 2.13 (0.21), residues: 621 sheet: 0.10 (0.69), residues: 52 loop : 0.54 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.003 0.001 HIS A 142 PHE 0.032 0.001 PHE A 513 TYR 0.012 0.001 TYR A1068 ARG 0.006 0.000 ARG A1147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.70 seconds wall clock time: 71 minutes 23.43 seconds (4283.43 seconds total)