Starting phenix.real_space_refine on Wed Mar 4 09:55:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cu3_30470/03_2026/7cu3_30470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cu3_30470/03_2026/7cu3_30470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cu3_30470/03_2026/7cu3_30470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cu3_30470/03_2026/7cu3_30470.map" model { file = "/net/cci-nas-00/data/ceres_data/7cu3_30470/03_2026/7cu3_30470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cu3_30470/03_2026/7cu3_30470.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 96 5.16 5 C 8092 2.51 5 N 1913 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12209 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1277, 10325 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 1231} Chain breaks: 5 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 2, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Conformer: "B" Number of residues, atoms: 1277, 10325 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 1231} Chain breaks: 5 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 2, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 bond proxies already assigned to first conformer: 10563 Chain: "B" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1379 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 477 Unusual residues: {'6OU': 12, 'CLR': 2, 'NAG': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'6OU:plan-3': 2, '6OU:plan-1': 5, '6OU:plan-2': 2} Unresolved non-hydrogen planarities: 33 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATHR A1387 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A1387 " occ=0.50 residue: pdb=" N AGLY A1388 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1388 " occ=0.50 residue: pdb=" N AGLU A1389 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A1389 " occ=0.50 residue: pdb=" N AASP A1390 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A1390 " occ=0.50 Time building chain proxies: 4.15, per 1000 atoms: 0.34 Number of scatterers: 12209 At special positions: 0 Unit cell: (157.795, 117.04, 114.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 8 15.00 O 2100 8.00 N 1913 7.00 C 8092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.04 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 270 " distance=1.99 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 370 " distance=2.03 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 A2001 " - " ASN A 210 " " NAG A2002 " - " ASN A1064 " " NAG A2003 " - " ASN A 216 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 773.6 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 71.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.876A pdb=" N HIS A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 64 through 91 removed outlier: 4.016A pdb=" N GLN A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 130 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.759A pdb=" N GLY A 140 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.784A pdb=" N ALA A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 163 through 200 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.501A pdb=" N SER A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.658A pdb=" N LEU A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.892A pdb=" N SER A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 336 removed outlier: 3.853A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 383 through 403 Processing helix chain 'A' and resid 416 through 441 Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.571A pdb=" N TYR A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.914A pdb=" N GLN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 505 through 529 Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 555 through 568 removed outlier: 3.505A pdb=" N GLY A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 603 removed outlier: 4.672A pdb=" N LEU A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.674A pdb=" N CYS A 850 " --> pdb=" O PHE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 883 removed outlier: 4.097A pdb=" N TYR A 879 " --> pdb=" O TYR A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 904 Processing helix chain 'A' and resid 915 through 941 removed outlier: 4.634A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 972 removed outlier: 3.522A pdb=" N VAL A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 990 Processing helix chain 'A' and resid 991 through 994 Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1000 through 1012 Processing helix chain 'A' and resid 1013 through 1040 removed outlier: 3.506A pdb=" N ALA A1040 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1113 removed outlier: 3.604A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1128 removed outlier: 3.522A pdb=" N VAL A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1132 through 1144 removed outlier: 3.830A pdb=" N ILE A1136 " --> pdb=" O HIS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1163 removed outlier: 3.758A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1183 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 4.311A pdb=" N MET A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1226 Processing helix chain 'A' and resid 1237 through 1263 removed outlier: 3.511A pdb=" N MET A1263 " --> pdb=" O LYS A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1269 removed outlier: 3.897A pdb=" N TRP A1269 " --> pdb=" O PRO A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1294 Processing helix chain 'A' and resid 1296 through 1314 removed outlier: 3.607A pdb=" N TYR A1300 " --> pdb=" O ASN A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1317 No H-bonds generated for 'chain 'A' and resid 1315 through 1317' Processing helix chain 'A' and resid 1318 through 1335 Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1374 through 1387 removed outlier: 3.744A pdb=" N VAL A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ATHR A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1398 Processing helix chain 'A' and resid 1411 through 1415 removed outlier: 3.627A pdb=" N ALA A1414 " --> pdb=" O THR A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1437 removed outlier: 3.570A pdb=" N ILE A1437 " --> pdb=" O ILE A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 3.934A pdb=" N LEU A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1478 Processing helix chain 'A' and resid 1487 through 1497 removed outlier: 3.888A pdb=" N LYS A1491 " --> pdb=" O THR A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1502 removed outlier: 3.575A pdb=" N LEU A1501 " --> pdb=" O ARG A1498 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A1502 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1502' Processing helix chain 'A' and resid 1508 through 1522 Processing helix chain 'A' and resid 1531 through 1541 Processing helix chain 'A' and resid 1543 through 1548 Processing helix chain 'A' and resid 1549 through 1578 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 268 through 297 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.664A pdb=" N SER B 301 " --> pdb=" O TYR B 298 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 302 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 326 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.720A pdb=" N LEU B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AA2, first strand: chain 'A' and resid 1045 through 1046 Processing sheet with id=AA3, first strand: chain 'A' and resid 1060 through 1064 732 hydrogen bonds defined for protein. 2154 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1824 1.30 - 1.43: 3428 1.43 - 1.56: 6967 1.56 - 1.68: 135 1.68 - 1.81: 149 Bond restraints: 12503 Sorted by residual: bond pdb=" C16 6OU A2010 " pdb=" O17 6OU A2010 " ideal model delta sigma weight residual 1.207 1.412 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C07 6OU A2010 " pdb=" C08 6OU A2010 " ideal model delta sigma weight residual 1.524 1.336 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C16 6OU A2010 " pdb=" O18 6OU A2010 " ideal model delta sigma weight residual 1.327 1.176 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C16 6OU A2006 " pdb=" O18 6OU A2006 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C16 6OU A2013 " pdb=" O18 6OU A2013 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.28e+01 ... (remaining 12498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 16574 3.33 - 6.65: 266 6.65 - 9.98: 37 9.98 - 13.31: 3 13.31 - 16.63: 8 Bond angle restraints: 16888 Sorted by residual: angle pdb=" O22 6OU A2006 " pdb=" P23 6OU A2006 " pdb=" O26 6OU A2006 " ideal model delta sigma weight residual 93.95 110.58 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O22 6OU A2015 " pdb=" P23 6OU A2015 " pdb=" O26 6OU A2015 " ideal model delta sigma weight residual 93.95 110.13 -16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O22 6OU A2014 " pdb=" P23 6OU A2014 " pdb=" O26 6OU A2014 " ideal model delta sigma weight residual 93.95 109.37 -15.42 3.00e+00 1.11e-01 2.64e+01 angle pdb=" O22 6OU A2013 " pdb=" P23 6OU A2013 " pdb=" O26 6OU A2013 " ideal model delta sigma weight residual 93.95 109.30 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" O22 6OU A2007 " pdb=" P23 6OU A2007 " pdb=" O26 6OU A2007 " ideal model delta sigma weight residual 93.95 109.05 -15.10 3.00e+00 1.11e-01 2.53e+01 ... (remaining 16883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 7287 35.29 - 70.58: 259 70.58 - 105.87: 41 105.87 - 141.16: 13 141.16 - 176.45: 9 Dihedral angle restraints: 7609 sinusoidal: 3330 harmonic: 4279 Sorted by residual: dihedral pdb=" CB CYS B 200 " pdb=" SG CYS B 200 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 153.59 -60.59 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CA BGLU A1389 " pdb=" C BGLU A1389 " pdb=" N BASP A1390 " pdb=" CA BASP A1390 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C15 6OU A2005 " pdb=" C16 6OU A2005 " pdb=" O18 6OU A2005 " pdb=" C19 6OU A2005 " ideal model delta sinusoidal sigma weight residual 175.68 -0.77 176.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1544 0.057 - 0.114: 323 0.114 - 0.170: 28 0.170 - 0.227: 10 0.227 - 0.284: 1 Chirality restraints: 1906 Sorted by residual: chirality pdb=" CA HIS A 471 " pdb=" N HIS A 471 " pdb=" C HIS A 471 " pdb=" CB HIS A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C13 CLR A2017 " pdb=" C12 CLR A2017 " pdb=" C14 CLR A2017 " pdb=" C17 CLR A2017 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN A 210 " pdb=" N ASN A 210 " pdb=" C ASN A 210 " pdb=" CB ASN A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1903 not shown) Planarity restraints: 2051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " 0.035 2.00e-02 2.50e+03 2.94e-02 1.08e+01 pdb=" C7 NAG A2001 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " -0.010 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " -0.046 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1136 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ILE A1136 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A1136 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A1137 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 586 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C ALA A 586 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA A 586 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 587 " 0.012 2.00e-02 2.50e+03 ... (remaining 2048 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1105 2.74 - 3.28: 12189 3.28 - 3.82: 21082 3.82 - 4.36: 25665 4.36 - 4.90: 42683 Nonbonded interactions: 102724 Sorted by model distance: nonbonded pdb=" O THR A 947 " pdb=" OG1 THR A 947 " model vdw 2.196 3.040 nonbonded pdb=" N ASP A 250 " pdb=" OD1 ASP A 250 " model vdw 2.212 3.120 nonbonded pdb=" O ASN A 404 " pdb=" NH2 ARG A 413 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR A1207 " pdb=" OE1 GLN A1208 " model vdw 2.261 3.040 nonbonded pdb=" O THR A1529 " pdb=" OG1 THR A1529 " model vdw 2.294 3.040 ... (remaining 102719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.900 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.205 12517 Z= 0.444 Angle : 1.038 38.411 16919 Z= 0.468 Chirality : 0.047 0.284 1906 Planarity : 0.005 0.046 2048 Dihedral : 19.751 176.455 4800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.43 % Allowed : 6.87 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1438 helix: -0.41 (0.15), residues: 963 sheet: 0.20 (1.62), residues: 12 loop : -2.72 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 481 TYR 0.020 0.002 TYR A1426 PHE 0.015 0.002 PHE A 184 TRP 0.016 0.002 TRP A1085 HIS 0.004 0.001 HIS A1132 Details of bonding type rmsd covalent geometry : bond 0.00935 (12503) covalent geometry : angle 0.99228 (16888) SS BOND : bond 0.01197 ( 11) SS BOND : angle 8.38394 ( 22) hydrogen bonds : bond 0.11767 ( 732) hydrogen bonds : angle 5.97501 ( 2154) link_NAG-ASN : bond 0.00452 ( 3) link_NAG-ASN : angle 2.10344 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.427 Fit side-chains REVERT: A 59 MET cc_start: 0.7500 (mmm) cc_final: 0.7297 (tpt) REVERT: A 108 CYS cc_start: 0.7075 (m) cc_final: 0.6775 (m) REVERT: A 235 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: A 380 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7573 (ppp) REVERT: A 409 GLU cc_start: 0.6592 (pt0) cc_final: 0.6189 (tt0) REVERT: A 415 TYR cc_start: 0.7815 (m-80) cc_final: 0.7358 (m-10) REVERT: A 432 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 757 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8470 (mm110) REVERT: A 851 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (ttm170) REVERT: A 903 MET cc_start: 0.8693 (mtp) cc_final: 0.8399 (mtm) REVERT: A 1003 MET cc_start: 0.8938 (mmm) cc_final: 0.8588 (mmm) REVERT: A 1009 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 1029 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7956 (tt) REVERT: A 1200 ARG cc_start: 0.7017 (mtm180) cc_final: 0.6777 (mtt180) REVERT: A 1270 GLN cc_start: 0.8002 (mt0) cc_final: 0.7696 (mm-40) REVERT: A 1318 HIS cc_start: 0.8042 (t-170) cc_final: 0.7832 (t-90) REVERT: A 1476 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6741 (ptp) REVERT: A 1491 LYS cc_start: 0.7346 (ptmm) cc_final: 0.6558 (ttpp) REVERT: A 1492 PHE cc_start: 0.7335 (m-80) cc_final: 0.6849 (m-80) REVERT: A 1509 LYS cc_start: 0.7912 (ttpm) cc_final: 0.7538 (mppt) REVERT: B 279 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: B 356 ASP cc_start: 0.8341 (t0) cc_final: 0.8108 (t0) outliers start: 44 outliers final: 15 residues processed: 241 average time/residue: 0.5434 time to fit residues: 142.8841 Evaluate side-chains 185 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 371 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 759 HIS A 934 ASN A1296 ASN A1449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105052 restraints weight = 24000.762| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.72 r_work: 0.3044 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12517 Z= 0.143 Angle : 0.568 12.167 16919 Z= 0.292 Chirality : 0.040 0.278 1906 Planarity : 0.005 0.044 2048 Dihedral : 20.003 161.762 2137 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.51 % Allowed : 11.24 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1438 helix: 1.08 (0.16), residues: 955 sheet: -0.91 (1.74), residues: 10 loop : -2.14 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 847 TYR 0.016 0.001 TYR A1426 PHE 0.013 0.001 PHE A 184 TRP 0.012 0.001 TRP A1287 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00322 (12503) covalent geometry : angle 0.56641 (16888) SS BOND : bond 0.00290 ( 11) SS BOND : angle 0.77502 ( 22) hydrogen bonds : bond 0.04642 ( 732) hydrogen bonds : angle 4.39865 ( 2154) link_NAG-ASN : bond 0.00231 ( 3) link_NAG-ASN : angle 1.77095 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.449 Fit side-chains REVERT: A 59 MET cc_start: 0.8151 (mmm) cc_final: 0.7915 (tpt) REVERT: A 72 PHE cc_start: 0.8228 (t80) cc_final: 0.8023 (t80) REVERT: A 108 CYS cc_start: 0.7621 (m) cc_final: 0.7311 (m) REVERT: A 235 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: A 380 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7307 (ppp) REVERT: A 388 MET cc_start: 0.7516 (mtt) cc_final: 0.6723 (tpt) REVERT: A 409 GLU cc_start: 0.6671 (pt0) cc_final: 0.6288 (tt0) REVERT: A 757 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8589 (mm110) REVERT: A 763 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6617 (pt0) REVERT: A 903 MET cc_start: 0.8960 (mtp) cc_final: 0.8738 (mtm) REVERT: A 1003 MET cc_start: 0.9072 (mmm) cc_final: 0.8737 (mmm) REVERT: A 1009 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8062 (mt-10) REVERT: A 1029 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8094 (tt) REVERT: A 1200 ARG cc_start: 0.7250 (mtm180) cc_final: 0.6946 (mtt180) REVERT: A 1244 MET cc_start: 0.8375 (mmp) cc_final: 0.7963 (mtp) REVERT: A 1270 GLN cc_start: 0.8043 (mt0) cc_final: 0.7665 (mm-40) REVERT: A 1302 MET cc_start: 0.8157 (ttm) cc_final: 0.7928 (ttt) REVERT: A 1334 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8631 (mttp) REVERT: A 1460 GLN cc_start: 0.7387 (pm20) cc_final: 0.7068 (mt0) REVERT: A 1462 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 1492 PHE cc_start: 0.7522 (m-80) cc_final: 0.7019 (m-80) REVERT: A 1509 LYS cc_start: 0.7847 (ttpm) cc_final: 0.7402 (mptt) REVERT: A 1510 LEU cc_start: 0.8404 (tp) cc_final: 0.8159 (tp) REVERT: B 279 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7568 (m-30) outliers start: 45 outliers final: 19 residues processed: 214 average time/residue: 0.5092 time to fit residues: 119.4029 Evaluate side-chains 195 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106646 restraints weight = 25007.823| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.79 r_work: 0.3063 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12517 Z= 0.116 Angle : 0.512 10.752 16919 Z= 0.264 Chirality : 0.038 0.221 1906 Planarity : 0.004 0.044 2048 Dihedral : 18.014 162.203 2124 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.12 % Allowed : 13.19 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1438 helix: 1.65 (0.17), residues: 953 sheet: -0.73 (1.84), residues: 10 loop : -1.86 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 271 TYR 0.014 0.001 TYR A1426 PHE 0.010 0.001 PHE A 184 TRP 0.012 0.001 TRP A1287 HIS 0.002 0.000 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00254 (12503) covalent geometry : angle 0.50966 (16888) SS BOND : bond 0.00171 ( 11) SS BOND : angle 0.66051 ( 22) hydrogen bonds : bond 0.04177 ( 732) hydrogen bonds : angle 4.16814 ( 2154) link_NAG-ASN : bond 0.00399 ( 3) link_NAG-ASN : angle 2.03101 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.399 Fit side-chains REVERT: A 59 MET cc_start: 0.8123 (mmm) cc_final: 0.7902 (tpt) REVERT: A 72 PHE cc_start: 0.8228 (t80) cc_final: 0.7995 (t80) REVERT: A 77 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 79 MET cc_start: 0.7865 (tmm) cc_final: 0.7277 (ppp) REVERT: A 80 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: A 108 CYS cc_start: 0.7527 (m) cc_final: 0.7232 (m) REVERT: A 235 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: A 275 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 284 PHE cc_start: 0.8324 (m-80) cc_final: 0.8036 (m-10) REVERT: A 388 MET cc_start: 0.7490 (mtt) cc_final: 0.6582 (tpt) REVERT: A 409 GLU cc_start: 0.6596 (pt0) cc_final: 0.6228 (tt0) REVERT: A 903 MET cc_start: 0.8948 (mtp) cc_final: 0.8734 (ttm) REVERT: A 975 ASN cc_start: 0.8761 (m-40) cc_final: 0.8527 (m-40) REVERT: A 1003 MET cc_start: 0.9049 (mmm) cc_final: 0.8666 (mmm) REVERT: A 1009 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 1244 MET cc_start: 0.8441 (mmp) cc_final: 0.8053 (mtp) REVERT: A 1270 GLN cc_start: 0.7984 (mt0) cc_final: 0.7592 (mm-40) REVERT: A 1302 MET cc_start: 0.8124 (ttm) cc_final: 0.7871 (ttm) REVERT: A 1460 GLN cc_start: 0.7400 (pm20) cc_final: 0.6926 (mt0) REVERT: A 1492 PHE cc_start: 0.7625 (m-80) cc_final: 0.7115 (m-80) REVERT: A 1509 LYS cc_start: 0.7842 (ttpm) cc_final: 0.7321 (mptt) REVERT: A 1510 LEU cc_start: 0.8378 (tp) cc_final: 0.8039 (tp) REVERT: B 279 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: B 336 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8082 (t) outliers start: 40 outliers final: 14 residues processed: 212 average time/residue: 0.4959 time to fit residues: 115.6909 Evaluate side-chains 196 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1208 GLN A1296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108756 restraints weight = 21221.509| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.66 r_work: 0.3114 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12517 Z= 0.104 Angle : 0.484 9.190 16919 Z= 0.250 Chirality : 0.037 0.190 1906 Planarity : 0.004 0.044 2048 Dihedral : 16.395 161.139 2111 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.65 % Allowed : 14.68 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1438 helix: 1.97 (0.17), residues: 949 sheet: -0.92 (1.78), residues: 10 loop : -1.66 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.013 0.001 TYR A1426 PHE 0.009 0.001 PHE A1031 TRP 0.010 0.001 TRP A1413 HIS 0.002 0.000 HIS A1523 Details of bonding type rmsd covalent geometry : bond 0.00220 (12503) covalent geometry : angle 0.48187 (16888) SS BOND : bond 0.00214 ( 11) SS BOND : angle 0.89032 ( 22) hydrogen bonds : bond 0.03831 ( 732) hydrogen bonds : angle 4.00442 ( 2154) link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 1.55484 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.415 Fit side-chains REVERT: A 37 TRP cc_start: 0.6372 (p-90) cc_final: 0.6105 (p-90) REVERT: A 59 MET cc_start: 0.8063 (mmm) cc_final: 0.7844 (tpt) REVERT: A 72 PHE cc_start: 0.8150 (t80) cc_final: 0.7903 (t80) REVERT: A 77 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7197 (mp) REVERT: A 79 MET cc_start: 0.7869 (tmm) cc_final: 0.7590 (pp-130) REVERT: A 108 CYS cc_start: 0.7479 (m) cc_final: 0.7124 (m) REVERT: A 127 PHE cc_start: 0.8167 (m-80) cc_final: 0.7953 (m-10) REVERT: A 141 MET cc_start: 0.8875 (mtp) cc_final: 0.8579 (mtt) REVERT: A 235 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: A 284 PHE cc_start: 0.8237 (m-80) cc_final: 0.8032 (m-10) REVERT: A 388 MET cc_start: 0.7454 (mtt) cc_final: 0.6550 (tpt) REVERT: A 409 GLU cc_start: 0.6569 (pt0) cc_final: 0.6250 (tt0) REVERT: A 877 GLN cc_start: 0.6635 (tp40) cc_final: 0.6378 (tp40) REVERT: A 880 ASP cc_start: 0.7753 (m-30) cc_final: 0.7014 (t0) REVERT: A 903 MET cc_start: 0.8906 (mtp) cc_final: 0.8697 (ttm) REVERT: A 958 ASP cc_start: 0.8231 (m-30) cc_final: 0.7944 (m-30) REVERT: A 975 ASN cc_start: 0.8748 (m-40) cc_final: 0.8533 (m-40) REVERT: A 1003 MET cc_start: 0.9006 (mmm) cc_final: 0.8755 (mmm) REVERT: A 1009 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 1029 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8161 (tm) REVERT: A 1167 LEU cc_start: 0.9160 (mt) cc_final: 0.8936 (tp) REVERT: A 1244 MET cc_start: 0.8444 (mmp) cc_final: 0.8050 (mtp) REVERT: A 1270 GLN cc_start: 0.7911 (mt0) cc_final: 0.7548 (mm-40) REVERT: A 1302 MET cc_start: 0.8074 (ttm) cc_final: 0.7775 (ttm) REVERT: A 1460 GLN cc_start: 0.7217 (pm20) cc_final: 0.6725 (mt0) REVERT: A 1492 PHE cc_start: 0.7660 (m-80) cc_final: 0.7137 (m-80) REVERT: A 1502 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6291 (tp30) REVERT: A 1509 LYS cc_start: 0.7787 (ttpm) cc_final: 0.7339 (mptt) REVERT: A 1510 LEU cc_start: 0.8407 (tp) cc_final: 0.8088 (tp) REVERT: A 1558 GLN cc_start: 0.7373 (tp40) cc_final: 0.6908 (tp-100) REVERT: A 1559 LEU cc_start: 0.8289 (tm) cc_final: 0.7980 (tt) REVERT: B 281 ASP cc_start: 0.8566 (t70) cc_final: 0.8166 (t70) outliers start: 34 outliers final: 16 residues processed: 210 average time/residue: 0.4813 time to fit residues: 111.7692 Evaluate side-chains 199 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 128 optimal weight: 0.0170 chunk 117 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109349 restraints weight = 17824.156| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.58 r_work: 0.3143 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12517 Z= 0.100 Angle : 0.478 8.708 16919 Z= 0.245 Chirality : 0.037 0.195 1906 Planarity : 0.004 0.044 2048 Dihedral : 15.467 159.461 2106 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.04 % Allowed : 14.99 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1438 helix: 2.09 (0.17), residues: 951 sheet: -1.51 (1.05), residues: 20 loop : -1.66 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 334 TYR 0.015 0.001 TYR A1517 PHE 0.008 0.001 PHE A1031 TRP 0.009 0.001 TRP A1413 HIS 0.002 0.000 HIS A1523 Details of bonding type rmsd covalent geometry : bond 0.00211 (12503) covalent geometry : angle 0.47611 (16888) SS BOND : bond 0.00212 ( 11) SS BOND : angle 0.70987 ( 22) hydrogen bonds : bond 0.03717 ( 732) hydrogen bonds : angle 3.93666 ( 2154) link_NAG-ASN : bond 0.00116 ( 3) link_NAG-ASN : angle 1.58461 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.472 Fit side-chains REVERT: A 37 TRP cc_start: 0.6402 (p-90) cc_final: 0.6163 (p-90) REVERT: A 59 MET cc_start: 0.8021 (mmm) cc_final: 0.7814 (tpt) REVERT: A 72 PHE cc_start: 0.8073 (t80) cc_final: 0.7852 (t80) REVERT: A 108 CYS cc_start: 0.7498 (m) cc_final: 0.7187 (m) REVERT: A 141 MET cc_start: 0.8817 (mtp) cc_final: 0.8550 (mtt) REVERT: A 388 MET cc_start: 0.7400 (mtt) cc_final: 0.6564 (tpt) REVERT: A 409 GLU cc_start: 0.6635 (pt0) cc_final: 0.6294 (tt0) REVERT: A 877 GLN cc_start: 0.6669 (tp40) cc_final: 0.6415 (tp40) REVERT: A 903 MET cc_start: 0.8880 (mtp) cc_final: 0.8667 (ttm) REVERT: A 958 ASP cc_start: 0.8135 (m-30) cc_final: 0.7853 (m-30) REVERT: A 1003 MET cc_start: 0.8989 (mmm) cc_final: 0.8725 (mmm) REVERT: A 1009 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 1029 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8237 (tm) REVERT: A 1167 LEU cc_start: 0.9133 (mt) cc_final: 0.8908 (tp) REVERT: A 1270 GLN cc_start: 0.7930 (mt0) cc_final: 0.7574 (mm-40) REVERT: A 1302 MET cc_start: 0.8020 (ttm) cc_final: 0.7743 (ttm) REVERT: A 1460 GLN cc_start: 0.7172 (pm20) cc_final: 0.6660 (mt0) REVERT: A 1480 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.5931 (mtmm) REVERT: A 1492 PHE cc_start: 0.7681 (m-80) cc_final: 0.7151 (m-80) REVERT: A 1502 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: A 1510 LEU cc_start: 0.8399 (tp) cc_final: 0.8182 (tp) REVERT: A 1559 LEU cc_start: 0.8251 (tm) cc_final: 0.8028 (tt) REVERT: B 281 ASP cc_start: 0.8509 (t70) cc_final: 0.8105 (t70) outliers start: 39 outliers final: 19 residues processed: 209 average time/residue: 0.4793 time to fit residues: 110.8865 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1365 ASN Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1480 LYS Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A 975 ASN A1296 ASN A1419 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105536 restraints weight = 25737.009| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.84 r_work: 0.3041 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12517 Z= 0.150 Angle : 0.540 10.386 16919 Z= 0.278 Chirality : 0.040 0.234 1906 Planarity : 0.004 0.045 2048 Dihedral : 15.646 167.211 2101 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.59 % Allowed : 14.99 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1438 helix: 1.94 (0.17), residues: 953 sheet: -1.33 (1.06), residues: 20 loop : -1.56 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 329 TYR 0.023 0.002 TYR A1426 PHE 0.012 0.001 PHE B 352 TRP 0.012 0.001 TRP A1287 HIS 0.003 0.001 HIS A1318 Details of bonding type rmsd covalent geometry : bond 0.00347 (12503) covalent geometry : angle 0.53729 (16888) SS BOND : bond 0.00313 ( 11) SS BOND : angle 1.30223 ( 22) hydrogen bonds : bond 0.04497 ( 732) hydrogen bonds : angle 4.10845 ( 2154) link_NAG-ASN : bond 0.00211 ( 3) link_NAG-ASN : angle 1.52065 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.454 Fit side-chains REVERT: A 37 TRP cc_start: 0.6401 (p-90) cc_final: 0.6154 (p-90) REVERT: A 59 MET cc_start: 0.8119 (mmm) cc_final: 0.7865 (tpt) REVERT: A 72 PHE cc_start: 0.8221 (t80) cc_final: 0.7990 (t80) REVERT: A 108 CYS cc_start: 0.7510 (m) cc_final: 0.7213 (m) REVERT: A 388 MET cc_start: 0.7522 (mtt) cc_final: 0.6564 (tpt) REVERT: A 409 GLU cc_start: 0.6685 (pt0) cc_final: 0.6337 (tt0) REVERT: A 527 MET cc_start: 0.8792 (mtm) cc_final: 0.8568 (mtp) REVERT: A 877 GLN cc_start: 0.6696 (tp40) cc_final: 0.6431 (tp40) REVERT: A 903 MET cc_start: 0.8932 (mtp) cc_final: 0.8699 (ttm) REVERT: A 958 ASP cc_start: 0.8288 (m-30) cc_final: 0.8048 (m-30) REVERT: A 1003 MET cc_start: 0.9065 (mmm) cc_final: 0.8829 (mmm) REVERT: A 1009 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 1029 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8238 (tm) REVERT: A 1167 LEU cc_start: 0.9119 (mt) cc_final: 0.8893 (tp) REVERT: A 1270 GLN cc_start: 0.8099 (mt0) cc_final: 0.7764 (mm-40) REVERT: A 1301 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7131 (tmm) REVERT: A 1492 PHE cc_start: 0.7655 (m-80) cc_final: 0.7168 (m-80) REVERT: A 1502 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6469 (tp30) REVERT: A 1509 LYS cc_start: 0.7918 (ttmp) cc_final: 0.7496 (mptt) REVERT: A 1510 LEU cc_start: 0.8427 (tp) cc_final: 0.7947 (tp) REVERT: A 1559 LEU cc_start: 0.8302 (tm) cc_final: 0.7996 (tt) REVERT: B 261 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4525 (mm) outliers start: 46 outliers final: 21 residues processed: 212 average time/residue: 0.4490 time to fit residues: 105.2493 Evaluate side-chains 201 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 122 optimal weight: 0.1980 chunk 134 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104659 restraints weight = 15852.896| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.48 r_work: 0.3057 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12517 Z= 0.142 Angle : 0.526 9.045 16919 Z= 0.272 Chirality : 0.039 0.211 1906 Planarity : 0.004 0.045 2048 Dihedral : 15.505 170.694 2101 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.97 % Allowed : 15.77 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1438 helix: 1.93 (0.17), residues: 953 sheet: -1.24 (1.08), residues: 20 loop : -1.52 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 334 TYR 0.021 0.001 TYR A1426 PHE 0.010 0.001 PHE A 184 TRP 0.012 0.001 TRP A1287 HIS 0.003 0.001 HIS A1132 Details of bonding type rmsd covalent geometry : bond 0.00330 (12503) covalent geometry : angle 0.52365 (16888) SS BOND : bond 0.00273 ( 11) SS BOND : angle 0.99286 ( 22) hydrogen bonds : bond 0.04383 ( 732) hydrogen bonds : angle 4.11806 ( 2154) link_NAG-ASN : bond 0.00186 ( 3) link_NAG-ASN : angle 1.58573 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.447 Fit side-chains REVERT: A 37 TRP cc_start: 0.6395 (p-90) cc_final: 0.6147 (p-90) REVERT: A 59 MET cc_start: 0.8070 (mmm) cc_final: 0.7818 (tpt) REVERT: A 108 CYS cc_start: 0.7518 (m) cc_final: 0.7219 (m) REVERT: A 141 MET cc_start: 0.8796 (mtp) cc_final: 0.8535 (mtp) REVERT: A 388 MET cc_start: 0.7456 (mtt) cc_final: 0.6542 (tpt) REVERT: A 409 GLU cc_start: 0.6695 (pt0) cc_final: 0.6336 (tt0) REVERT: A 527 MET cc_start: 0.8766 (mtm) cc_final: 0.8490 (mtp) REVERT: A 877 GLN cc_start: 0.6640 (tp40) cc_final: 0.6347 (tp40) REVERT: A 903 MET cc_start: 0.8905 (mtp) cc_final: 0.8666 (ttm) REVERT: A 958 ASP cc_start: 0.8203 (m-30) cc_final: 0.7958 (m-30) REVERT: A 1003 MET cc_start: 0.9033 (mmm) cc_final: 0.8757 (mmm) REVERT: A 1009 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 1029 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8298 (tm) REVERT: A 1270 GLN cc_start: 0.8105 (mt0) cc_final: 0.7800 (mm-40) REVERT: A 1301 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7049 (tmm) REVERT: A 1302 MET cc_start: 0.8110 (ttm) cc_final: 0.7856 (ttm) REVERT: A 1492 PHE cc_start: 0.7647 (m-80) cc_final: 0.7162 (m-80) REVERT: A 1502 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6446 (tp30) REVERT: A 1509 LYS cc_start: 0.7836 (ttmp) cc_final: 0.7391 (mptt) REVERT: A 1510 LEU cc_start: 0.8331 (tp) cc_final: 0.8121 (tt) REVERT: A 1559 LEU cc_start: 0.8332 (tm) cc_final: 0.8026 (tt) REVERT: B 261 LEU cc_start: 0.4823 (OUTLIER) cc_final: 0.4581 (mm) REVERT: B 277 TYR cc_start: 0.8560 (m-10) cc_final: 0.8339 (m-10) outliers start: 38 outliers final: 26 residues processed: 205 average time/residue: 0.4559 time to fit residues: 103.6960 Evaluate side-chains 209 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1296 ASN B 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108173 restraints weight = 25472.473| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.84 r_work: 0.3090 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12517 Z= 0.106 Angle : 0.492 7.772 16919 Z= 0.253 Chirality : 0.037 0.175 1906 Planarity : 0.004 0.044 2048 Dihedral : 14.837 167.373 2101 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.89 % Allowed : 16.16 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1438 helix: 2.08 (0.17), residues: 955 sheet: -1.16 (1.11), residues: 20 loop : -1.42 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 847 TYR 0.015 0.001 TYR A1426 PHE 0.009 0.001 PHE A1031 TRP 0.011 0.001 TRP A1287 HIS 0.002 0.000 HIS A1523 Details of bonding type rmsd covalent geometry : bond 0.00230 (12503) covalent geometry : angle 0.48909 (16888) SS BOND : bond 0.00198 ( 11) SS BOND : angle 0.89155 ( 22) hydrogen bonds : bond 0.03880 ( 732) hydrogen bonds : angle 4.00701 ( 2154) link_NAG-ASN : bond 0.00177 ( 3) link_NAG-ASN : angle 1.85293 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6380 (p-90) cc_final: 0.6142 (p-90) REVERT: A 59 MET cc_start: 0.8115 (mmm) cc_final: 0.7892 (tpt) REVERT: A 108 CYS cc_start: 0.7571 (m) cc_final: 0.7312 (m) REVERT: A 388 MET cc_start: 0.7518 (mtt) cc_final: 0.6602 (tpt) REVERT: A 409 GLU cc_start: 0.6678 (pt0) cc_final: 0.6325 (tt0) REVERT: A 527 MET cc_start: 0.8739 (mtm) cc_final: 0.8484 (mtp) REVERT: A 844 HIS cc_start: 0.3658 (OUTLIER) cc_final: 0.3247 (p-80) REVERT: A 877 GLN cc_start: 0.6644 (tp40) cc_final: 0.6361 (tp40) REVERT: A 880 ASP cc_start: 0.7743 (m-30) cc_final: 0.7269 (t0) REVERT: A 903 MET cc_start: 0.8902 (mtp) cc_final: 0.8699 (ttm) REVERT: A 958 ASP cc_start: 0.8218 (m-30) cc_final: 0.7966 (m-30) REVERT: A 1003 MET cc_start: 0.9044 (mmm) cc_final: 0.8833 (mmm) REVERT: A 1009 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 1029 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8276 (tm) REVERT: A 1270 GLN cc_start: 0.8087 (mt0) cc_final: 0.7742 (mm-40) REVERT: A 1302 MET cc_start: 0.8101 (ttm) cc_final: 0.7820 (ttm) REVERT: A 1492 PHE cc_start: 0.7654 (m-80) cc_final: 0.7155 (m-80) REVERT: A 1502 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: A 1510 LEU cc_start: 0.8350 (tp) cc_final: 0.8071 (tp) REVERT: B 261 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4607 (mm) outliers start: 37 outliers final: 23 residues processed: 208 average time/residue: 0.4641 time to fit residues: 106.7980 Evaluate side-chains 206 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.0270 chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108549 restraints weight = 20678.732| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.64 r_work: 0.3114 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12517 Z= 0.105 Angle : 0.486 7.553 16919 Z= 0.251 Chirality : 0.037 0.165 1906 Planarity : 0.004 0.043 2048 Dihedral : 14.231 163.567 2101 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.26 % Allowed : 17.02 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.23), residues: 1438 helix: 2.13 (0.17), residues: 957 sheet: -1.18 (1.11), residues: 20 loop : -1.44 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1521 TYR 0.016 0.001 TYR A1426 PHE 0.009 0.001 PHE A1031 TRP 0.010 0.001 TRP B 241 HIS 0.002 0.001 HIS A1523 Details of bonding type rmsd covalent geometry : bond 0.00227 (12503) covalent geometry : angle 0.48418 (16888) SS BOND : bond 0.00204 ( 11) SS BOND : angle 0.86414 ( 22) hydrogen bonds : bond 0.03824 ( 732) hydrogen bonds : angle 3.95229 ( 2154) link_NAG-ASN : bond 0.00115 ( 3) link_NAG-ASN : angle 1.64515 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6394 (p-90) cc_final: 0.6155 (p-90) REVERT: A 59 MET cc_start: 0.8066 (mmm) cc_final: 0.7840 (tpt) REVERT: A 108 CYS cc_start: 0.7542 (m) cc_final: 0.7265 (m) REVERT: A 141 MET cc_start: 0.8723 (mtp) cc_final: 0.8472 (mtp) REVERT: A 379 LYS cc_start: 0.7022 (tttt) cc_final: 0.6586 (ptpp) REVERT: A 388 MET cc_start: 0.7428 (mtt) cc_final: 0.6538 (tpt) REVERT: A 409 GLU cc_start: 0.6654 (pt0) cc_final: 0.6294 (tt0) REVERT: A 527 MET cc_start: 0.8715 (mtm) cc_final: 0.8457 (mtp) REVERT: A 844 HIS cc_start: 0.3564 (OUTLIER) cc_final: 0.3190 (p-80) REVERT: A 877 GLN cc_start: 0.6707 (tp40) cc_final: 0.6433 (tp40) REVERT: A 880 ASP cc_start: 0.7766 (m-30) cc_final: 0.7282 (t0) REVERT: A 903 MET cc_start: 0.8897 (mtp) cc_final: 0.8688 (ttm) REVERT: A 958 ASP cc_start: 0.8166 (m-30) cc_final: 0.7908 (m-30) REVERT: A 1003 MET cc_start: 0.9042 (mmm) cc_final: 0.8813 (mmm) REVERT: A 1009 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 1029 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8157 (tm) REVERT: A 1270 GLN cc_start: 0.8077 (mt0) cc_final: 0.7736 (mm-40) REVERT: A 1302 MET cc_start: 0.8062 (ttm) cc_final: 0.7782 (ttm) REVERT: A 1492 PHE cc_start: 0.7654 (m-80) cc_final: 0.7128 (m-80) REVERT: A 1502 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: A 1558 GLN cc_start: 0.7313 (tp40) cc_final: 0.6840 (tp-100) REVERT: B 261 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4703 (mm) outliers start: 29 outliers final: 21 residues processed: 200 average time/residue: 0.4853 time to fit residues: 107.2636 Evaluate side-chains 206 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 119 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.0050 overall best weight: 0.6070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1514 HIS B 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107240 restraints weight = 16617.355| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.54 r_work: 0.3134 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12517 Z= 0.098 Angle : 0.481 9.243 16919 Z= 0.246 Chirality : 0.037 0.148 1906 Planarity : 0.004 0.043 2048 Dihedral : 13.819 165.683 2101 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.03 % Allowed : 17.56 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1438 helix: 2.25 (0.17), residues: 950 sheet: -1.18 (1.12), residues: 20 loop : -1.40 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1310 TYR 0.014 0.001 TYR A1426 PHE 0.009 0.001 PHE A1031 TRP 0.010 0.001 TRP B 241 HIS 0.002 0.000 HIS A1523 Details of bonding type rmsd covalent geometry : bond 0.00204 (12503) covalent geometry : angle 0.47957 (16888) SS BOND : bond 0.00140 ( 11) SS BOND : angle 0.74197 ( 22) hydrogen bonds : bond 0.03650 ( 732) hydrogen bonds : angle 3.90338 ( 2154) link_NAG-ASN : bond 0.00122 ( 3) link_NAG-ASN : angle 1.62326 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6395 (p-90) cc_final: 0.6161 (p-90) REVERT: A 59 MET cc_start: 0.8050 (mmm) cc_final: 0.7816 (tpt) REVERT: A 108 CYS cc_start: 0.7534 (m) cc_final: 0.7238 (m) REVERT: A 379 LYS cc_start: 0.7023 (tttt) cc_final: 0.6525 (ptpp) REVERT: A 388 MET cc_start: 0.7385 (mtt) cc_final: 0.6510 (tpt) REVERT: A 409 GLU cc_start: 0.6589 (pt0) cc_final: 0.6229 (tt0) REVERT: A 434 LEU cc_start: 0.8669 (mt) cc_final: 0.8388 (mt) REVERT: A 527 MET cc_start: 0.8702 (mtm) cc_final: 0.8488 (mtp) REVERT: A 877 GLN cc_start: 0.6662 (tp40) cc_final: 0.6388 (tp40) REVERT: A 880 ASP cc_start: 0.7876 (m-30) cc_final: 0.7412 (t0) REVERT: A 958 ASP cc_start: 0.8124 (m-30) cc_final: 0.7835 (m-30) REVERT: A 1003 MET cc_start: 0.8997 (mmm) cc_final: 0.8766 (mmm) REVERT: A 1009 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 1029 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8165 (tm) REVERT: A 1270 GLN cc_start: 0.8015 (mt0) cc_final: 0.7660 (mm-40) REVERT: A 1302 MET cc_start: 0.8021 (ttm) cc_final: 0.7738 (ttm) REVERT: A 1360 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 1492 PHE cc_start: 0.7659 (m-80) cc_final: 0.7122 (m-80) REVERT: A 1502 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6227 (tp30) REVERT: A 1558 GLN cc_start: 0.7286 (tp40) cc_final: 0.6805 (tp-100) REVERT: B 261 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.4658 (mm) REVERT: B 281 ASP cc_start: 0.8521 (t70) cc_final: 0.8149 (t70) outliers start: 26 outliers final: 16 residues processed: 200 average time/residue: 0.4851 time to fit residues: 107.1462 Evaluate side-chains 196 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105751 restraints weight = 25888.580| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.90 r_work: 0.3041 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12517 Z= 0.144 Angle : 0.534 8.993 16919 Z= 0.275 Chirality : 0.039 0.179 1906 Planarity : 0.004 0.044 2048 Dihedral : 14.148 167.043 2101 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.19 % Allowed : 17.49 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1438 helix: 2.12 (0.17), residues: 948 sheet: -0.84 (1.80), residues: 10 loop : -1.33 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 334 TYR 0.022 0.002 TYR A1426 PHE 0.011 0.001 PHE B 352 TRP 0.011 0.001 TRP A1287 HIS 0.003 0.001 HIS A1396 Details of bonding type rmsd covalent geometry : bond 0.00334 (12503) covalent geometry : angle 0.52896 (16888) SS BOND : bond 0.00272 ( 11) SS BOND : angle 1.86843 ( 22) hydrogen bonds : bond 0.04283 ( 732) hydrogen bonds : angle 4.03900 ( 2154) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.52100 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.48 seconds wall clock time: 92 minutes 20.69 seconds (5540.69 seconds total)