Starting phenix.real_space_refine on Sat Dec 28 09:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0g_42854/12_2024/8v0g_42854_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0g_42854/12_2024/8v0g_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_42854/12_2024/8v0g_42854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0g_42854/12_2024/8v0g_42854.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0g_42854/12_2024/8v0g_42854_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0g_42854/12_2024/8v0g_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.87, per 1000 atoms: 0.72 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: 2.58 Conformation dependent library (CDL) restraints added in 939.9 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: 1.01 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: 2.97 Time building geometry restraints manager: 2.89 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.600 Find NCS groups from input model: 0.270 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: 29.560 ------------------------------------------------------------------------------- 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 : 0.973 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: 0.2100 time to fit residues: 84.3855 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 : 0.949 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 1.086 Fit side-chains revert: symmetry clash REVERT: A 352 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9147 (pt) REVERT: A 735 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 1398 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8064 (mtm180) outliers start: 25 outliers final: 9 residues processed: 206 average time/residue: 0.1895 time to fit residues: 56.8178 Evaluate side-chains 154 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 352 ILE 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 49 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8298 Z= 0.228 Angle : 0.589 9.419 11208 Z= 0.312 Chirality : 0.042 0.203 1265 Planarity : 0.004 0.043 1382 Dihedral : 7.017 90.225 1172 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.20 % Allowed : 15.14 % Favored : 81.66 % 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: 2.04 (0.27), residues: 975 helix: 2.09 (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 0.011 0.001 TRP A 726 HIS 0.005 0.001 HIS A1195 PHE 0.017 0.002 PHE A 733 TYR 0.015 0.001 TYR A 304 ARG 0.004 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 201 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.881 Fit side-chains REVERT: A 136 LEU cc_start: 0.8629 (tp) cc_final: 0.8368 (tt) REVERT: A 145 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8768 (mppt) REVERT: A 156 GLU cc_start: 0.7788 (tp30) cc_final: 0.7489 (tp30) REVERT: A 352 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9104 (pt) REVERT: A 735 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 1398 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8010 (mtm180) outliers start: 29 outliers final: 14 residues processed: 189 average time/residue: 0.1724 time to fit residues: 46.7651 Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 352 ILE 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 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 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 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 15 GLN A 142 HIS ** 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** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4307 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= 0.216 Angle : 0.574 10.280 11208 Z= 0.302 Chirality : 0.041 0.183 1265 Planarity : 0.004 0.039 1382 Dihedral : 6.593 80.604 1172 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.98 % Allowed : 16.24 % Favored : 79.78 % 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: 2.12 (0.26), residues: 975 helix: 2.15 (0.20), residues: 618 sheet: -0.32 (0.65), residues: 52 loop : 0.26 (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 A 142 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 185 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.866 Fit side-chains REVERT: A 136 LEU cc_start: 0.8637 (tp) cc_final: 0.8312 (tt) REVERT: A 156 GLU cc_start: 0.7799 (tp30) cc_final: 0.7569 (tp30) REVERT: A 352 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9086 (pt) REVERT: A 735 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 1398 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7995 (mtm180) REVERT: A 1459 LEU cc_start: 0.9157 (tp) cc_final: 0.8957 (tp) outliers start: 36 outliers final: 17 residues processed: 172 average time/residue: 0.1651 time to fit residues: 41.1317 Evaluate side-chains 153 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 324 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 425 THR 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 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1206 SER 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 53 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8298 Z= 0.200 Angle : 0.573 11.019 11208 Z= 0.299 Chirality : 0.040 0.157 1265 Planarity : 0.004 0.037 1382 Dihedral : 6.079 68.132 1172 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.43 % Allowed : 17.02 % Favored : 79.56 % 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: 2.16 (0.27), residues: 975 helix: 2.18 (0.20), residues: 618 sheet: -0.28 (0.65), residues: 52 loop : 0.27 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.018 0.001 PHE A 665 TYR 0.016 0.001 TYR A 369 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 194 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 352 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8968 (pp) REVERT: A 735 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 1398 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8008 (mtm180) REVERT: A 1459 LEU cc_start: 0.9136 (tp) cc_final: 0.8923 (tp) outliers start: 31 outliers final: 19 residues processed: 181 average time/residue: 0.1783 time to fit residues: 46.4499 Evaluate side-chains 162 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 52 CYS 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 352 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.0040 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 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** A1188 GLN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8298 Z= 0.196 Angle : 0.588 11.058 11208 Z= 0.303 Chirality : 0.040 0.182 1265 Planarity : 0.003 0.037 1382 Dihedral : 5.333 61.542 1172 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.20 % Allowed : 18.78 % Favored : 78.01 % 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: 2.11 (0.27), residues: 975 helix: 2.13 (0.20), residues: 620 sheet: -0.23 (0.65), residues: 52 loop : 0.23 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.024 0.001 PHE A 733 TYR 0.017 0.001 TYR A 55 ARG 0.004 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 187 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 352 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 1398 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (mtm180) REVERT: A 1459 LEU cc_start: 0.9149 (tp) cc_final: 0.8933 (tp) outliers start: 29 outliers final: 18 residues processed: 177 average time/residue: 0.1665 time to fit residues: 43.1984 Evaluate side-chains 165 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 352 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8298 Z= 0.208 Angle : 0.565 8.430 11208 Z= 0.297 Chirality : 0.041 0.222 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.684 57.508 1172 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.98 % Allowed : 19.23 % Favored : 77.79 % 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: 2.11 (0.27), residues: 975 helix: 2.12 (0.21), residues: 621 sheet: -0.19 (0.65), residues: 52 loop : 0.27 (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 A 142 PHE 0.022 0.001 PHE A 733 TYR 0.012 0.001 TYR A 67 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 185 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 156 GLU cc_start: 0.7776 (tp30) cc_final: 0.7509 (tp30) REVERT: A 352 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8962 (pp) REVERT: A 367 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8888 (tt) REVERT: A 457 ASP cc_start: 0.8048 (p0) cc_final: 0.7608 (m-30) REVERT: A 1398 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8000 (mtm180) REVERT: A 1459 LEU cc_start: 0.9164 (tp) cc_final: 0.8938 (tp) outliers start: 27 outliers final: 16 residues processed: 172 average time/residue: 0.1753 time to fit residues: 43.1929 Evaluate side-chains 163 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 352 ILE Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 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 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 37 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8298 Z= 0.211 Angle : 0.616 13.595 11208 Z= 0.317 Chirality : 0.041 0.209 1265 Planarity : 0.004 0.036 1382 Dihedral : 4.508 53.715 1172 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.76 % Allowed : 20.55 % 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: 2.17 (0.27), residues: 975 helix: 2.12 (0.20), residues: 620 sheet: -0.17 (0.66), residues: 52 loop : 0.41 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.030 0.001 PHE A 513 TYR 0.012 0.001 TYR A 67 ARG 0.005 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 180 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 352 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8970 (pp) REVERT: A 367 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8876 (tt) REVERT: A 458 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 1459 LEU cc_start: 0.9153 (tp) cc_final: 0.8929 (tp) outliers start: 25 outliers final: 18 residues processed: 171 average time/residue: 0.1582 time to fit residues: 40.0705 Evaluate side-chains 168 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 458 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 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 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** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8298 Z= 0.199 Angle : 0.605 16.410 11208 Z= 0.311 Chirality : 0.042 0.206 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.413 49.760 1172 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.87 % Allowed : 20.33 % Favored : 76.80 % 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: 2.10 (0.20), residues: 621 sheet: -0.12 (0.67), residues: 52 loop : 0.44 (0.36), 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 0.028 0.001 PHE A 513 TYR 0.013 0.001 TYR A 67 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 179 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 1398 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8004 (mtm180) REVERT: A 1459 LEU cc_start: 0.9144 (tp) cc_final: 0.8921 (tp) outliers start: 26 outliers final: 18 residues processed: 171 average time/residue: 0.1696 time to fit residues: 42.0883 Evaluate side-chains 172 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 352 ILE 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 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 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 ASN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5314 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= 0.191 Angle : 0.642 18.013 11208 Z= 0.323 Chirality : 0.041 0.206 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.362 46.595 1172 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.43 % Allowed : 21.55 % Favored : 76.02 % 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: 2.09 (0.21), residues: 622 sheet: -0.02 (0.68), residues: 52 loop : 0.52 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.033 0.001 PHE A 513 TYR 0.013 0.001 TYR A 67 ARG 0.004 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 183 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8929 (pp) REVERT: A 1398 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (mtm180) REVERT: A 1459 LEU cc_start: 0.9124 (tp) cc_final: 0.8915 (tp) outliers start: 22 outliers final: 17 residues processed: 175 average time/residue: 0.1738 time to fit residues: 44.3906 Evaluate side-chains 170 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 352 ILE 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 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 82 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** 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 = 0.3327 r_free = 0.3327 target = 0.089625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073378 restraints weight = 18341.922| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.23 r_work: 0.2943 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5362 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= 0.217 Angle : 0.637 18.376 11208 Z= 0.321 Chirality : 0.042 0.220 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.357 44.125 1172 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.32 % Allowed : 21.55 % Favored : 76.13 % 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: 2.14 (0.27), residues: 975 helix: 1.99 (0.21), residues: 628 sheet: 0.06 (0.69), residues: 52 loop : 0.57 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.032 0.001 PHE A 513 TYR 0.013 0.001 TYR A 67 ARG 0.004 0.000 ARG A1147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.84 seconds wall clock time: 38 minutes 50.18 seconds (2330.18 seconds total)