Starting phenix.real_space_refine on Wed Jul 30 19:46:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cu3_30470/07_2025/7cu3_30470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cu3_30470/07_2025/7cu3_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_30470/07_2025/7cu3_30470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cu3_30470/07_2025/7cu3_30470.map" model { file = "/net/cci-nas-00/data/ceres_data/7cu3_30470/07_2025/7cu3_30470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cu3_30470/07_2025/7cu3_30470.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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-1': 5, '6OU:plan-2': 2, '6OU:plan-3': 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: 12.50, per 1000 atoms: 1.02 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: 3.32 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.38 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: 4.41 Time building geometry restraints manager: 3.98 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: 1.000 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (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 TRP 0.016 0.002 TRP A1085 HIS 0.004 0.001 HIS A1132 PHE 0.015 0.002 PHE A 184 TYR 0.020 0.002 TYR A1426 ARG 0.004 0.001 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 3) link_NAG-ASN : angle 2.10344 ( 9) hydrogen bonds : bond 0.11767 ( 732) hydrogen bonds : angle 5.97501 ( 2154) SS BOND : bond 0.01197 ( 11) SS BOND : angle 8.38394 ( 22) covalent geometry : bond 0.00935 (12503) covalent geometry : angle 0.99228 (16888) *********************** 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 : 1.262 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: 0.8068 (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: 1.3916 time to fit residues: 370.2122 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 : 1.331 ------------------------------------------------------------------------------- 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 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.135094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106818 restraints weight = 23622.646| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.73 r_work: 0.3070 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12517 Z= 0.119 Angle : 0.540 11.740 16919 Z= 0.277 Chirality : 0.039 0.265 1906 Planarity : 0.005 0.042 2048 Dihedral : 19.569 158.545 2137 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.12 % Allowed : 11.55 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1438 helix: 1.19 (0.16), residues: 954 sheet: -0.98 (1.72), residues: 10 loop : -2.07 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 241 HIS 0.003 0.001 HIS A 206 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A1426 ARG 0.004 0.000 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 3) link_NAG-ASN : angle 1.68312 ( 9) hydrogen bonds : bond 0.04277 ( 732) hydrogen bonds : angle 4.33097 ( 2154) SS BOND : bond 0.00178 ( 11) SS BOND : angle 0.68299 ( 22) covalent geometry : bond 0.00247 (12503) covalent geometry : angle 0.53829 (16888) *********************** 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 231 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.252 Fit side-chains REVERT: A 72 PHE cc_start: 0.8153 (t80) cc_final: 0.7912 (t80) REVERT: A 108 CYS cc_start: 0.7590 (m) cc_final: 0.7254 (m) REVERT: A 235 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: A 380 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (ppp) REVERT: A 388 MET cc_start: 0.7522 (mtt) cc_final: 0.6750 (tpt) REVERT: A 409 GLU cc_start: 0.6644 (pt0) cc_final: 0.6264 (tt0) REVERT: A 757 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8605 (mm110) REVERT: A 763 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6573 (pt0) REVERT: A 1003 MET cc_start: 0.9071 (mmm) cc_final: 0.8749 (mmm) REVERT: A 1009 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 1029 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 1200 ARG cc_start: 0.7247 (mtm180) cc_final: 0.6969 (mtt180) REVERT: A 1244 MET cc_start: 0.8352 (mmp) cc_final: 0.7945 (mtp) REVERT: A 1270 GLN cc_start: 0.7989 (mt0) cc_final: 0.7624 (mm-40) REVERT: A 1302 MET cc_start: 0.8110 (ttm) cc_final: 0.7857 (ttm) REVERT: A 1334 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8768 (mttp) REVERT: A 1460 GLN cc_start: 0.7398 (pm20) cc_final: 0.7099 (mt0) REVERT: A 1492 PHE cc_start: 0.7500 (m-80) cc_final: 0.6960 (m-80) REVERT: A 1502 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: A 1509 LYS cc_start: 0.7803 (ttpm) cc_final: 0.7380 (mptt) REVERT: A 1510 LEU cc_start: 0.8358 (tp) cc_final: 0.7945 (tp) REVERT: B 279 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7708 (m-30) outliers start: 40 outliers final: 14 residues processed: 216 average time/residue: 1.1186 time to fit residues: 265.4574 Evaluate side-chains 192 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 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 1029 LEU 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 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 A1208 GLN A1296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107702 restraints weight = 25203.740| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.80 r_work: 0.3058 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 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 = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12517 Z= 0.109 Angle : 0.501 10.091 16919 Z= 0.257 Chirality : 0.038 0.212 1906 Planarity : 0.004 0.044 2048 Dihedral : 17.415 157.740 2119 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.73 % Allowed : 14.21 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1438 helix: 1.73 (0.17), residues: 955 sheet: -1.47 (1.09), residues: 20 loop : -1.89 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1287 HIS 0.002 0.001 HIS A1523 PHE 0.009 0.001 PHE A 184 TYR 0.014 0.001 TYR A1517 ARG 0.005 0.000 ARG A 382 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 2.32565 ( 9) hydrogen bonds : bond 0.04014 ( 732) hydrogen bonds : angle 4.07552 ( 2154) SS BOND : bond 0.00170 ( 11) SS BOND : angle 0.70358 ( 22) covalent geometry : bond 0.00232 (12503) covalent geometry : angle 0.49809 (16888) *********************** 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 223 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.246 Fit side-chains REVERT: A 37 TRP cc_start: 0.6361 (p-90) cc_final: 0.6091 (p-90) REVERT: A 72 PHE cc_start: 0.8154 (t80) cc_final: 0.7933 (t80) REVERT: A 79 MET cc_start: 0.7854 (tmm) cc_final: 0.7385 (ppp) REVERT: A 108 CYS cc_start: 0.7486 (m) cc_final: 0.7173 (m) REVERT: A 235 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: A 251 LEU cc_start: 0.6257 (mt) cc_final: 0.6037 (mm) REVERT: A 284 PHE cc_start: 0.8312 (m-80) cc_final: 0.8071 (m-10) REVERT: A 380 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7288 (ppp) REVERT: A 381 MET cc_start: 0.6801 (ttt) cc_final: 0.6600 (ptt) REVERT: A 388 MET cc_start: 0.7496 (mtt) cc_final: 0.6554 (tpt) REVERT: A 409 GLU cc_start: 0.6574 (pt0) cc_final: 0.6207 (tt0) REVERT: A 877 GLN cc_start: 0.6677 (tp40) cc_final: 0.6432 (tp40) REVERT: A 880 ASP cc_start: 0.7775 (m-30) cc_final: 0.7022 (t0) REVERT: A 958 ASP cc_start: 0.8263 (m-30) cc_final: 0.7955 (m-30) REVERT: A 1003 MET cc_start: 0.9025 (mmm) cc_final: 0.8764 (mmm) REVERT: A 1009 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 1244 MET cc_start: 0.8407 (mmp) cc_final: 0.7991 (mtp) REVERT: A 1270 GLN cc_start: 0.7908 (mt0) cc_final: 0.7547 (mm-40) REVERT: A 1302 MET cc_start: 0.8083 (ttm) cc_final: 0.7824 (ttm) REVERT: A 1334 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8687 (mttp) REVERT: A 1460 GLN cc_start: 0.7387 (pm20) cc_final: 0.6902 (mt0) REVERT: A 1492 PHE cc_start: 0.7645 (m-80) cc_final: 0.7124 (m-80) REVERT: A 1502 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6397 (tp30) REVERT: A 1509 LYS cc_start: 0.7821 (ttpm) cc_final: 0.7349 (mptt) REVERT: A 1510 LEU cc_start: 0.8368 (tp) cc_final: 0.8071 (tp) REVERT: A 1558 GLN cc_start: 0.7428 (tp40) cc_final: 0.6970 (tp-100) REVERT: B 281 ASP cc_start: 0.8591 (t70) cc_final: 0.8207 (t70) outliers start: 35 outliers final: 13 residues processed: 208 average time/residue: 1.0230 time to fit residues: 235.9128 Evaluate side-chains 196 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 235 GLU Chi-restraints excluded: chain A residue 380 MET 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 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 1502 GLU Chi-restraints excluded: chain B residue 249 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 120 optimal weight: 0.0000 chunk 77 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106796 restraints weight = 21762.154| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.68 r_work: 0.3083 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12517 Z= 0.122 Angle : 0.505 9.447 16919 Z= 0.262 Chirality : 0.038 0.218 1906 Planarity : 0.004 0.045 2048 Dihedral : 16.522 161.369 2107 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.28 % Allowed : 14.99 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1438 helix: 1.94 (0.17), residues: 947 sheet: -1.01 (1.75), residues: 10 loop : -1.72 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1287 HIS 0.003 0.001 HIS A1132 PHE 0.011 0.001 PHE A 184 TYR 0.018 0.001 TYR A1426 ARG 0.003 0.000 ARG A 382 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 3) link_NAG-ASN : angle 1.51542 ( 9) hydrogen bonds : bond 0.04175 ( 732) hydrogen bonds : angle 4.05997 ( 2154) SS BOND : bond 0.00265 ( 11) SS BOND : angle 0.91296 ( 22) covalent geometry : bond 0.00274 (12503) covalent geometry : angle 0.50362 (16888) *********************** 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 222 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.423 Fit side-chains REVERT: A 37 TRP cc_start: 0.6437 (p-90) cc_final: 0.6182 (p-90) REVERT: A 72 PHE cc_start: 0.8179 (t80) cc_final: 0.7921 (t80) REVERT: A 108 CYS cc_start: 0.7464 (m) cc_final: 0.7157 (m) REVERT: A 141 MET cc_start: 0.8823 (mtp) cc_final: 0.8555 (mtp) REVERT: A 284 PHE cc_start: 0.8342 (m-80) cc_final: 0.8109 (m-10) REVERT: A 380 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7183 (ppp) REVERT: A 381 MET cc_start: 0.6841 (ttt) cc_final: 0.6611 (ptt) REVERT: A 388 MET cc_start: 0.7500 (mtt) cc_final: 0.6567 (tpt) REVERT: A 409 GLU cc_start: 0.6680 (pt0) cc_final: 0.6297 (tt0) REVERT: A 877 GLN cc_start: 0.6687 (tp40) cc_final: 0.6449 (tp40) REVERT: A 880 ASP cc_start: 0.7800 (m-30) cc_final: 0.7055 (t0) REVERT: A 958 ASP cc_start: 0.8266 (m-30) cc_final: 0.7936 (m-30) REVERT: A 1003 MET cc_start: 0.9013 (mmm) cc_final: 0.8768 (mmm) REVERT: A 1009 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 1029 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8197 (tm) REVERT: A 1167 LEU cc_start: 0.9156 (mt) cc_final: 0.8953 (tp) REVERT: A 1244 MET cc_start: 0.8507 (mmp) cc_final: 0.8117 (mtp) REVERT: A 1270 GLN cc_start: 0.7970 (mt0) cc_final: 0.7585 (mm-40) REVERT: A 1301 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.7052 (tmm) REVERT: A 1302 MET cc_start: 0.8119 (ttm) cc_final: 0.7858 (ttm) REVERT: A 1334 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8682 (mttp) REVERT: A 1492 PHE cc_start: 0.7641 (m-80) cc_final: 0.7167 (m-80) REVERT: A 1502 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6419 (tp30) REVERT: A 1509 LYS cc_start: 0.7833 (ttpm) cc_final: 0.7402 (mptt) REVERT: A 1510 LEU cc_start: 0.8426 (tp) cc_final: 0.8124 (tp) REVERT: A 1558 GLN cc_start: 0.7435 (tp40) cc_final: 0.6971 (tp-100) REVERT: A 1564 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 336 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8104 (t) outliers start: 42 outliers final: 16 residues processed: 206 average time/residue: 1.1913 time to fit residues: 272.0585 Evaluate side-chains 199 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 380 MET 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 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 1334 LYS 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 B residue 249 SER Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 VAL 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 124 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 A1524 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108262 restraints weight = 24841.620| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.78 r_work: 0.3095 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12517 Z= 0.102 Angle : 0.483 9.374 16919 Z= 0.248 Chirality : 0.037 0.178 1906 Planarity : 0.004 0.044 2048 Dihedral : 15.812 160.809 2104 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.73 % Allowed : 15.61 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1438 helix: 2.06 (0.17), residues: 949 sheet: -1.00 (1.73), residues: 10 loop : -1.60 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1287 HIS 0.002 0.000 HIS A1291 PHE 0.009 0.001 PHE A1031 TYR 0.013 0.001 TYR A1426 ARG 0.002 0.000 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 3) link_NAG-ASN : angle 1.55247 ( 9) hydrogen bonds : bond 0.03854 ( 732) hydrogen bonds : angle 3.97617 ( 2154) SS BOND : bond 0.00184 ( 11) SS BOND : angle 0.75340 ( 22) covalent geometry : bond 0.00216 (12503) covalent geometry : angle 0.48114 (16888) *********************** 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 220 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.386 Fit side-chains REVERT: A 37 TRP cc_start: 0.6422 (p-90) cc_final: 0.6170 (p-90) REVERT: A 72 PHE cc_start: 0.8146 (t80) cc_final: 0.7913 (t80) REVERT: A 108 CYS cc_start: 0.7596 (m) cc_final: 0.7323 (m) REVERT: A 380 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7335 (tmm) REVERT: A 381 MET cc_start: 0.6805 (ttt) cc_final: 0.6569 (ptt) REVERT: A 388 MET cc_start: 0.7520 (mtt) cc_final: 0.6632 (tpt) REVERT: A 409 GLU cc_start: 0.6703 (pt0) cc_final: 0.6354 (tt0) REVERT: A 877 GLN cc_start: 0.6703 (tp40) cc_final: 0.6463 (tp40) REVERT: A 880 ASP cc_start: 0.7778 (m-30) cc_final: 0.7065 (t0) REVERT: A 958 ASP cc_start: 0.8217 (m-30) cc_final: 0.7940 (m-30) REVERT: A 1003 MET cc_start: 0.9016 (mmm) cc_final: 0.8778 (mmm) REVERT: A 1009 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 1029 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8147 (tm) REVERT: A 1270 GLN cc_start: 0.7966 (mt0) cc_final: 0.7600 (mm-40) REVERT: A 1302 MET cc_start: 0.8087 (ttm) cc_final: 0.7811 (ttm) REVERT: A 1334 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8681 (mttp) REVERT: A 1492 PHE cc_start: 0.7691 (m-80) cc_final: 0.7200 (m-80) REVERT: A 1502 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: A 1509 LYS cc_start: 0.7896 (ttpm) cc_final: 0.7408 (mppt) REVERT: A 1510 LEU cc_start: 0.8356 (tp) cc_final: 0.8132 (tp) REVERT: A 1558 GLN cc_start: 0.7399 (tp40) cc_final: 0.6968 (tp-100) REVERT: B 281 ASP cc_start: 0.8564 (t70) cc_final: 0.8199 (t70) REVERT: B 336 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8106 (t) REVERT: B 360 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7458 (t) outliers start: 35 outliers final: 17 residues processed: 206 average time/residue: 1.1443 time to fit residues: 260.5029 Evaluate side-chains 201 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 380 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL 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 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 1334 LYS 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 B residue 249 SER Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 122 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.138284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110081 restraints weight = 23608.489| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.72 r_work: 0.3123 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12517 Z= 0.098 Angle : 0.475 7.937 16919 Z= 0.245 Chirality : 0.037 0.158 1906 Planarity : 0.004 0.043 2048 Dihedral : 14.962 158.716 2104 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.04 % Allowed : 15.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1438 helix: 2.20 (0.17), residues: 950 sheet: -1.24 (1.06), residues: 20 loop : -1.60 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 241 HIS 0.002 0.000 HIS A1523 PHE 0.008 0.001 PHE A1031 TYR 0.016 0.001 TYR A1517 ARG 0.004 0.000 ARG A1481 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 3) link_NAG-ASN : angle 1.48939 ( 9) hydrogen bonds : bond 0.03641 ( 732) hydrogen bonds : angle 3.88801 ( 2154) SS BOND : bond 0.00157 ( 11) SS BOND : angle 0.68263 ( 22) covalent geometry : bond 0.00201 (12503) covalent geometry : angle 0.47380 (16888) *********************** 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: 39 poor density : 190 time to evaluate : 1.254 Fit side-chains REVERT: A 37 TRP cc_start: 0.6374 (p-90) cc_final: 0.6145 (p-90) REVERT: A 72 PHE cc_start: 0.8104 (t80) cc_final: 0.7856 (t80) REVERT: A 91 HIS cc_start: 0.6883 (t-90) cc_final: 0.6660 (t-170) REVERT: A 108 CYS cc_start: 0.7568 (m) cc_final: 0.7291 (m) REVERT: A 141 MET cc_start: 0.8721 (mtp) cc_final: 0.8462 (mtp) REVERT: A 388 MET cc_start: 0.7438 (mtt) cc_final: 0.6579 (tpt) REVERT: A 409 GLU cc_start: 0.6683 (pt0) cc_final: 0.6333 (tt0) REVERT: A 877 GLN cc_start: 0.6690 (tp40) cc_final: 0.6434 (tp40) REVERT: A 880 ASP cc_start: 0.7752 (m-30) cc_final: 0.7062 (t0) REVERT: A 958 ASP cc_start: 0.8178 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1003 MET cc_start: 0.9021 (mmm) cc_final: 0.8772 (mmm) REVERT: A 1009 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 1029 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8158 (tm) REVERT: A 1263 MET cc_start: 0.6426 (ptp) cc_final: 0.6136 (ptp) REVERT: A 1270 GLN cc_start: 0.7987 (mt0) cc_final: 0.7635 (mm-40) REVERT: A 1302 MET cc_start: 0.8060 (ttm) cc_final: 0.7791 (ttm) REVERT: A 1482 GLU cc_start: 0.6756 (mp0) cc_final: 0.6556 (mp0) REVERT: A 1492 PHE cc_start: 0.7717 (m-80) cc_final: 0.7188 (m-80) REVERT: A 1509 LYS cc_start: 0.7890 (ttpm) cc_final: 0.7416 (mptt) REVERT: A 1510 LEU cc_start: 0.8338 (tp) cc_final: 0.8001 (tp) REVERT: A 1558 GLN cc_start: 0.7333 (tp40) cc_final: 0.6900 (tp-100) REVERT: A 1559 LEU cc_start: 0.8182 (tm) cc_final: 0.7968 (tt) REVERT: B 261 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.4675 (mm) REVERT: B 277 TYR cc_start: 0.8609 (m-10) cc_final: 0.8398 (m-10) REVERT: B 281 ASP cc_start: 0.8535 (t70) cc_final: 0.8179 (t70) outliers start: 39 outliers final: 17 residues processed: 214 average time/residue: 1.2523 time to fit residues: 297.2223 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 : 1.614 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL 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 1233 VAL 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 B residue 249 SER Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 123 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 0.1980 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 0.0870 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.140012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111108 restraints weight = 19006.338| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.75 r_work: 0.3148 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 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 = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12517 Z= 0.096 Angle : 0.470 9.077 16919 Z= 0.243 Chirality : 0.036 0.138 1906 Planarity : 0.004 0.042 2048 Dihedral : 14.317 163.201 2101 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.03 % Allowed : 16.86 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.23), residues: 1438 helix: 2.38 (0.17), residues: 942 sheet: -1.20 (1.09), residues: 20 loop : -1.42 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1413 HIS 0.002 0.000 HIS A1291 PHE 0.008 0.001 PHE A1031 TYR 0.015 0.001 TYR A1517 ARG 0.003 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 1.43804 ( 9) hydrogen bonds : bond 0.03437 ( 732) hydrogen bonds : angle 3.81921 ( 2154) SS BOND : bond 0.00186 ( 11) SS BOND : angle 0.59508 ( 22) covalent geometry : bond 0.00198 (12503) covalent geometry : angle 0.46913 (16888) *********************** 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 215 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.886 Fit side-chains REVERT: A 37 TRP cc_start: 0.6336 (p-90) cc_final: 0.6067 (p-90) REVERT: A 72 PHE cc_start: 0.8034 (t80) cc_final: 0.7827 (t80) REVERT: A 79 MET cc_start: 0.7916 (tmm) cc_final: 0.7452 (ppp) REVERT: A 91 HIS cc_start: 0.6868 (t-90) cc_final: 0.6652 (t-170) REVERT: A 108 CYS cc_start: 0.7482 (m) cc_final: 0.7214 (m) REVERT: A 141 MET cc_start: 0.8732 (mtp) cc_final: 0.8505 (mtp) REVERT: A 275 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 379 LYS cc_start: 0.7081 (tttt) cc_final: 0.6505 (ptpp) REVERT: A 381 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6277 (ptt) REVERT: A 388 MET cc_start: 0.7400 (mtt) cc_final: 0.6569 (tpt) REVERT: A 409 GLU cc_start: 0.6663 (pt0) cc_final: 0.6326 (tt0) REVERT: A 434 LEU cc_start: 0.8675 (mt) cc_final: 0.8416 (mt) REVERT: A 877 GLN cc_start: 0.6685 (tp40) cc_final: 0.6418 (tp40) REVERT: A 880 ASP cc_start: 0.7732 (m-30) cc_final: 0.7201 (t0) REVERT: A 1003 MET cc_start: 0.8971 (mmm) cc_final: 0.8716 (mmm) REVERT: A 1270 GLN cc_start: 0.7967 (mt0) cc_final: 0.7610 (mm-40) REVERT: A 1302 MET cc_start: 0.8006 (ttm) cc_final: 0.7748 (ttm) REVERT: A 1360 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8846 (p) REVERT: A 1482 GLU cc_start: 0.6634 (mp0) cc_final: 0.5010 (tt0) REVERT: A 1492 PHE cc_start: 0.7705 (m-80) cc_final: 0.7188 (m-80) REVERT: A 1509 LYS cc_start: 0.7843 (ttpm) cc_final: 0.7363 (mptt) REVERT: A 1510 LEU cc_start: 0.8290 (tp) cc_final: 0.8088 (tt) REVERT: A 1558 GLN cc_start: 0.7299 (tp40) cc_final: 0.6867 (tp-100) REVERT: B 277 TYR cc_start: 0.8503 (m-10) cc_final: 0.8263 (m-10) REVERT: B 281 ASP cc_start: 0.8533 (t70) cc_final: 0.8174 (t70) outliers start: 26 outliers final: 13 residues processed: 206 average time/residue: 1.5775 time to fit residues: 359.6365 Evaluate side-chains 186 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 381 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 8.9990 chunk 78 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 A1419 ASN A1514 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109402 restraints weight = 19682.252| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.67 r_work: 0.3126 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2430 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= 0.104 Angle : 0.490 8.789 16919 Z= 0.251 Chirality : 0.037 0.149 1906 Planarity : 0.004 0.043 2048 Dihedral : 14.145 164.620 2101 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.34 % Allowed : 17.95 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1438 helix: 2.29 (0.17), residues: 951 sheet: -1.20 (1.10), residues: 20 loop : -1.53 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1287 HIS 0.002 0.001 HIS A1291 PHE 0.008 0.001 PHE B 352 TYR 0.016 0.001 TYR A1517 ARG 0.003 0.000 ARG A1053 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 3) link_NAG-ASN : angle 1.77719 ( 9) hydrogen bonds : bond 0.03714 ( 732) hydrogen bonds : angle 3.86036 ( 2154) SS BOND : bond 0.00183 ( 11) SS BOND : angle 1.00558 ( 22) covalent geometry : bond 0.00227 (12503) covalent geometry : angle 0.48731 (16888) *********************** 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 207 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6324 (p-90) cc_final: 0.6110 (p-90) REVERT: A 72 PHE cc_start: 0.8067 (t80) cc_final: 0.7858 (t80) REVERT: A 79 MET cc_start: 0.7928 (tmm) cc_final: 0.7452 (ppp) REVERT: A 91 HIS cc_start: 0.6876 (t-90) cc_final: 0.6661 (t-170) REVERT: A 108 CYS cc_start: 0.7507 (m) cc_final: 0.7203 (m) REVERT: A 141 MET cc_start: 0.8752 (mtp) cc_final: 0.8496 (mtp) REVERT: A 379 LYS cc_start: 0.6932 (tttt) cc_final: 0.6492 (ttpp) REVERT: A 388 MET cc_start: 0.7369 (mtt) cc_final: 0.6511 (tpt) REVERT: A 409 GLU cc_start: 0.6658 (pt0) cc_final: 0.6318 (tt0) REVERT: A 434 LEU cc_start: 0.8633 (mt) cc_final: 0.8404 (mt) REVERT: A 877 GLN cc_start: 0.6682 (tp40) cc_final: 0.6408 (tp40) REVERT: A 880 ASP cc_start: 0.7780 (m-30) cc_final: 0.7225 (t0) REVERT: A 1003 MET cc_start: 0.9036 (mmm) cc_final: 0.8806 (mmm) REVERT: A 1270 GLN cc_start: 0.7997 (mt0) cc_final: 0.7652 (mm-40) REVERT: A 1302 MET cc_start: 0.8020 (ttm) cc_final: 0.7760 (ttm) REVERT: A 1360 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 1492 PHE cc_start: 0.7664 (m-80) cc_final: 0.7111 (m-80) REVERT: A 1510 LEU cc_start: 0.8346 (tp) cc_final: 0.8124 (tp) REVERT: A 1558 GLN cc_start: 0.7282 (tp40) cc_final: 0.6830 (tp-100) REVERT: B 261 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4589 (mm) REVERT: B 277 TYR cc_start: 0.8572 (m-10) cc_final: 0.8330 (m-10) REVERT: B 281 ASP cc_start: 0.8552 (t70) cc_final: 0.8191 (t70) outliers start: 30 outliers final: 15 residues processed: 198 average time/residue: 1.1172 time to fit residues: 245.6604 Evaluate side-chains 189 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 1007 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 1424 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 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 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 B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102835 restraints weight = 17094.812| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.57 r_work: 0.3068 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12517 Z= 0.152 Angle : 0.547 8.871 16919 Z= 0.283 Chirality : 0.040 0.206 1906 Planarity : 0.004 0.044 2048 Dihedral : 14.617 168.040 2101 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.95 % Allowed : 18.03 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1438 helix: 2.06 (0.17), residues: 954 sheet: -0.88 (1.79), residues: 10 loop : -1.50 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.003 0.001 HIS A 206 PHE 0.012 0.001 PHE A1139 TYR 0.024 0.002 TYR A1426 ARG 0.002 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 3) link_NAG-ASN : angle 1.64876 ( 9) hydrogen bonds : bond 0.04510 ( 732) hydrogen bonds : angle 4.09653 ( 2154) SS BOND : bond 0.00305 ( 11) SS BOND : angle 1.15225 ( 22) covalent geometry : bond 0.00354 (12503) covalent geometry : angle 0.54457 (16888) *********************** 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 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6408 (p-90) cc_final: 0.6171 (p-90) REVERT: A 141 MET cc_start: 0.8827 (mtp) cc_final: 0.8539 (mtp) REVERT: A 379 LYS cc_start: 0.6857 (tttt) cc_final: 0.6416 (ptpp) REVERT: A 388 MET cc_start: 0.7482 (mtt) cc_final: 0.6537 (tpt) REVERT: A 409 GLU cc_start: 0.6648 (pt0) cc_final: 0.6285 (tt0) REVERT: A 877 GLN cc_start: 0.6542 (tp40) cc_final: 0.6270 (tp40) REVERT: A 1003 MET cc_start: 0.9048 (mmm) cc_final: 0.8808 (mmm) REVERT: A 1029 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8317 (tm) REVERT: A 1270 GLN cc_start: 0.8097 (mt0) cc_final: 0.7775 (mm-40) REVERT: A 1302 MET cc_start: 0.8143 (ttm) cc_final: 0.7872 (ttm) REVERT: A 1492 PHE cc_start: 0.7632 (m-80) cc_final: 0.7144 (m-80) REVERT: A 1510 LEU cc_start: 0.8391 (tp) cc_final: 0.8162 (tt) REVERT: B 261 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4564 (mm) outliers start: 25 outliers final: 16 residues processed: 193 average time/residue: 1.0126 time to fit residues: 216.2835 Evaluate side-chains 191 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU 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 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 334 ARG 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 4 optimal weight: 2.9990 chunk 88 optimal weight: 0.0010 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.137839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.108431 restraints weight = 18019.478| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.65 r_work: 0.3128 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 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 = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2439 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= 0.100 Angle : 0.495 8.405 16919 Z= 0.254 Chirality : 0.037 0.147 1906 Planarity : 0.004 0.043 2048 Dihedral : 13.778 164.150 2101 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.33 % Allowed : 18.89 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1438 helix: 2.25 (0.17), residues: 949 sheet: -1.17 (1.12), residues: 20 loop : -1.46 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1413 HIS 0.003 0.001 HIS A1523 PHE 0.009 0.001 PHE A1031 TYR 0.015 0.001 TYR A1517 ARG 0.004 0.000 ARG A1053 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 3) link_NAG-ASN : angle 1.71441 ( 9) hydrogen bonds : bond 0.03655 ( 732) hydrogen bonds : angle 3.92524 ( 2154) SS BOND : bond 0.00144 ( 11) SS BOND : angle 0.80536 ( 22) covalent geometry : bond 0.00205 (12503) covalent geometry : angle 0.49302 (16888) ********************** 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 199 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6359 (p-90) cc_final: 0.6129 (p-90) REVERT: A 141 MET cc_start: 0.8732 (mtp) cc_final: 0.8511 (mtp) REVERT: A 379 LYS cc_start: 0.6810 (tttt) cc_final: 0.6457 (ptpp) REVERT: A 388 MET cc_start: 0.7455 (mtt) cc_final: 0.6555 (tpt) REVERT: A 409 GLU cc_start: 0.6635 (pt0) cc_final: 0.6256 (tt0) REVERT: A 877 GLN cc_start: 0.6597 (tp40) cc_final: 0.6332 (tp40) REVERT: A 880 ASP cc_start: 0.7747 (m-30) cc_final: 0.7291 (t0) REVERT: A 1003 MET cc_start: 0.9012 (mmm) cc_final: 0.8687 (mmm) REVERT: A 1029 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8254 (tm) REVERT: A 1270 GLN cc_start: 0.8005 (mt0) cc_final: 0.7679 (mm-40) REVERT: A 1302 MET cc_start: 0.8044 (ttm) cc_final: 0.7767 (ttm) REVERT: A 1360 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8859 (p) REVERT: A 1492 PHE cc_start: 0.7650 (m-80) cc_final: 0.7119 (m-80) REVERT: A 1510 LEU cc_start: 0.8349 (tp) cc_final: 0.8102 (tp) REVERT: B 277 TYR cc_start: 0.8497 (m-10) cc_final: 0.8282 (m-10) outliers start: 17 outliers final: 13 residues processed: 193 average time/residue: 1.2291 time to fit residues: 263.6044 Evaluate side-chains 187 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 1029 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.136632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107855 restraints weight = 20602.547| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.68 r_work: 0.3094 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12517 Z= 0.115 Angle : 0.512 9.365 16919 Z= 0.264 Chirality : 0.038 0.161 1906 Planarity : 0.004 0.043 2048 Dihedral : 13.770 164.574 2101 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.48 % Allowed : 18.66 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1438 helix: 2.23 (0.17), residues: 950 sheet: -1.33 (1.08), residues: 20 loop : -1.45 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1287 HIS 0.002 0.001 HIS A1132 PHE 0.009 0.001 PHE B 352 TYR 0.017 0.001 TYR A1426 ARG 0.003 0.000 ARG A1053 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 3) link_NAG-ASN : angle 1.56509 ( 9) hydrogen bonds : bond 0.03895 ( 732) hydrogen bonds : angle 3.93738 ( 2154) SS BOND : bond 0.00218 ( 11) SS BOND : angle 2.18942 ( 22) covalent geometry : bond 0.00259 (12503) covalent geometry : angle 0.50536 (16888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12593.91 seconds wall clock time: 224 minutes 22.81 seconds (13462.81 seconds total)