Starting phenix.real_space_refine on Fri Aug 22 22:12:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlc_36392/08_2025/8jlc_36392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlc_36392/08_2025/8jlc_36392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jlc_36392/08_2025/8jlc_36392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlc_36392/08_2025/8jlc_36392.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlc_36392/08_2025/8jlc_36392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlc_36392/08_2025/8jlc_36392.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5291 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.28 Number of scatterers: 8189 At special positions: 0 Unit cell: (87.98, 85.49, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1489 8.00 N 1362 7.00 C 5291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG F 1 " - " ASN A 573 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 424.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 44.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 4.099A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Proline residue: A 191 - end of helix removed outlier: 4.316A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.965A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.911A pdb=" N PHE A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.319A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.525A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.766A pdb=" N LYS A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.802A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.754A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.577A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 593 through 623 Proline residue: A 610 - end of helix removed outlier: 5.245A pdb=" N ASP A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 641 removed outlier: 3.678A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.720A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 removed outlier: 3.567A pdb=" N PHE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.760A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1210 through 1215 removed outlier: 4.235A pdb=" N VAL B1214 " --> pdb=" O ILE B1211 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY B1215 " --> pdb=" O PRO B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 485 through 492 current: chain 'A' and resid 515 through 527 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'B' and resid 1142 through 1144 Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884 removed outlier: 3.590A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 887 through 890 current: chain 'B' and resid 914 through 916 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 916 current: chain 'B' and resid 1015 through 1021 removed outlier: 4.000A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA4, first strand: chain 'B' and resid 962 through 966 removed outlier: 6.724A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA6, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AA7, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.119A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1189 through 1194 current: chain 'B' and resid 1232 through 1240 removed outlier: 27.387A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.558A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.950A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1771 1.33 - 1.47: 3037 1.47 - 1.61: 3497 1.61 - 1.75: 3 1.75 - 1.89: 75 Bond restraints: 8383 Sorted by residual: bond pdb=" C GLY A 591 " pdb=" N GLU A 592 " ideal model delta sigma weight residual 1.335 1.458 -0.123 1.35e-02 5.49e+03 8.37e+01 bond pdb=" C5 UKX A 803 " pdb=" C6 UKX A 803 " ideal model delta sigma weight residual 1.533 1.709 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C GLY A 604 " pdb=" O GLY A 604 " ideal model delta sigma weight residual 1.233 1.290 -0.057 1.17e-02 7.31e+03 2.40e+01 bond pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 1.458 1.517 -0.059 1.30e-02 5.92e+03 2.07e+01 bond pdb=" C VAL A 171 " pdb=" O VAL A 171 " ideal model delta sigma weight residual 1.237 1.285 -0.048 1.13e-02 7.83e+03 1.82e+01 ... (remaining 8378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 11091 3.17 - 6.35: 231 6.35 - 9.52: 11 9.52 - 12.69: 1 12.69 - 15.87: 1 Bond angle restraints: 11335 Sorted by residual: angle pdb=" C GLY A 591 " pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 120.60 136.47 -15.87 1.60e+00 3.91e-01 9.84e+01 angle pdb=" OD1 ASN A 498 " pdb=" CG ASN A 498 " pdb=" ND2 ASN A 498 " ideal model delta sigma weight residual 122.60 116.64 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" N VAL A 671 " pdb=" CA VAL A 671 " pdb=" C VAL A 671 " ideal model delta sigma weight residual 110.62 115.27 -4.65 1.02e+00 9.61e-01 2.08e+01 angle pdb=" CA ASP B1256 " pdb=" CB ASP B1256 " pdb=" CG ASP B1256 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N ILE B1148 " pdb=" CA ILE B1148 " pdb=" C ILE B1148 " ideal model delta sigma weight residual 111.62 108.13 3.49 7.90e-01 1.60e+00 1.95e+01 ... (remaining 11330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 4439 15.69 - 31.38: 423 31.38 - 47.07: 75 47.07 - 62.76: 15 62.76 - 78.45: 12 Dihedral angle restraints: 4964 sinusoidal: 2041 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N MET B1054 " pdb=" CA MET B1054 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU B1210 " pdb=" C GLU B1210 " pdb=" N ILE B1211 " pdb=" CA ILE B1211 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 1237 0.252 - 0.504: 6 0.504 - 0.755: 0 0.755 - 1.007: 0 1.007 - 1.259: 1 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C1 FUC F 3 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 3 " pdb=" O5 FUC F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.32e+01 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.67e+01 ... (remaining 1241 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 467 " 0.067 2.00e-02 2.50e+03 5.61e-02 7.88e+01 pdb=" CG TRP A 467 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 467 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP A 467 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 467 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP A 467 " 0.076 2.00e-02 2.50e+03 pdb=" CE3 TRP A 467 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 467 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 467 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 467 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 548 " 0.066 2.00e-02 2.50e+03 7.39e-02 6.82e+01 pdb=" CG ASN A 548 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 548 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 548 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " -0.073 2.00e-02 2.50e+03 6.05e-02 4.57e+01 pdb=" C7 NAG A 802 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " 0.098 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.011 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 613 2.74 - 3.28: 8249 3.28 - 3.82: 13731 3.82 - 4.36: 16864 4.36 - 4.90: 28701 Nonbonded interactions: 68158 Sorted by model distance: nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.195 3.120 nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.228 3.040 nonbonded pdb=" NE2 GLN A 323 " pdb=" O GLY A 325 " model vdw 2.272 3.120 nonbonded pdb=" OD1 ASP A 470 " pdb=" NH2 ARG A 473 " model vdw 2.288 3.120 ... (remaining 68153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 0.011 0.226 8388 Z= 0.678 Angle : 1.275 34.306 11350 Z= 0.791 Chirality : 0.086 1.259 1244 Planarity : 0.011 0.149 1428 Dihedral : 13.035 78.450 3098 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1006 helix: 1.06 (0.25), residues: 405 sheet: -0.08 (0.33), residues: 241 loop : -1.33 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG B1140 TYR 0.053 0.009 TYR A 169 PHE 0.068 0.011 PHE A 299 TRP 0.085 0.012 TRP A 467 HIS 0.013 0.004 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.01068 ( 8383) covalent geometry : angle 1.18478 (11335) hydrogen bonds : bond 0.13527 ( 374) hydrogen bonds : angle 5.89288 ( 1077) link_BETA1-4 : bond 0.00096 ( 1) link_BETA1-4 : angle 1.68604 ( 3) link_BETA1-6 : bond 0.01775 ( 1) link_BETA1-6 : angle 1.37472 ( 3) link_NAG-ASN : bond 0.14410 ( 3) link_NAG-ASN : angle 16.76596 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5741 (mtp85) REVERT: A 197 MET cc_start: 0.6566 (mtm) cc_final: 0.5263 (tpt) REVERT: A 227 ASP cc_start: 0.8194 (m-30) cc_final: 0.7914 (m-30) REVERT: A 366 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6283 (mttm) REVERT: A 372 MET cc_start: 0.7261 (mtm) cc_final: 0.7027 (mmm) REVERT: A 444 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6245 (ttt180) REVERT: A 491 ARG cc_start: 0.7519 (tmt170) cc_final: 0.7252 (tmt170) REVERT: A 520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7509 (tmm-80) REVERT: A 542 SER cc_start: 0.8059 (t) cc_final: 0.7844 (t) REVERT: A 563 GLU cc_start: 0.8138 (pt0) cc_final: 0.7196 (tp30) REVERT: A 567 VAL cc_start: 0.7421 (t) cc_final: 0.7180 (t) REVERT: A 568 ASN cc_start: 0.8211 (t0) cc_final: 0.7877 (p0) REVERT: A 581 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 910 ASP cc_start: 0.5165 (t0) cc_final: 0.4352 (t0) REVERT: B 925 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 1097 LEU cc_start: 0.6800 (mm) cc_final: 0.6475 (tt) REVERT: B 1127 ASN cc_start: 0.8545 (m-40) cc_final: 0.8332 (p0) REVERT: B 1219 GLN cc_start: 0.7566 (pt0) cc_final: 0.6767 (pt0) REVERT: B 1246 ASP cc_start: 0.7038 (p0) cc_final: 0.6704 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.6587 time to fit residues: 122.0523 Evaluate side-chains 131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 434 ASN A 513 ASN B1073 ASN B1115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.223990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144547 restraints weight = 8866.002| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.61 r_work: 0.3462 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8388 Z= 0.138 Angle : 0.617 14.060 11350 Z= 0.314 Chirality : 0.046 0.455 1244 Planarity : 0.003 0.033 1428 Dihedral : 6.232 56.581 1221 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.28 % Allowed : 9.33 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.27), residues: 1006 helix: 1.95 (0.25), residues: 408 sheet: 0.13 (0.34), residues: 231 loop : -1.16 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 903 TYR 0.017 0.001 TYR B1191 PHE 0.016 0.001 PHE A 512 TRP 0.019 0.002 TRP A 300 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8383) covalent geometry : angle 0.57902 (11335) hydrogen bonds : bond 0.05196 ( 374) hydrogen bonds : angle 4.77055 ( 1077) link_BETA1-4 : bond 0.00420 ( 1) link_BETA1-4 : angle 0.97300 ( 3) link_BETA1-6 : bond 0.00553 ( 1) link_BETA1-6 : angle 1.21581 ( 3) link_NAG-ASN : bond 0.00599 ( 3) link_NAG-ASN : angle 7.54607 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7793 (tm-30) REVERT: A 197 MET cc_start: 0.6754 (mtm) cc_final: 0.6124 (ttm) REVERT: A 366 LYS cc_start: 0.7343 (mtmt) cc_final: 0.6731 (mttm) REVERT: A 372 MET cc_start: 0.7588 (mtm) cc_final: 0.6985 (mmm) REVERT: A 379 ASP cc_start: 0.6226 (m-30) cc_final: 0.5948 (m-30) REVERT: A 444 ARG cc_start: 0.6924 (ttp-110) cc_final: 0.6654 (ttt180) REVERT: A 491 ARG cc_start: 0.7540 (tmt170) cc_final: 0.7237 (tpt-90) REVERT: A 497 PHE cc_start: 0.7964 (m-80) cc_final: 0.7725 (m-10) REVERT: A 522 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7452 (tppt) REVERT: A 563 GLU cc_start: 0.8137 (pt0) cc_final: 0.7491 (tp30) REVERT: A 567 VAL cc_start: 0.8559 (t) cc_final: 0.8175 (m) REVERT: A 568 ASN cc_start: 0.8326 (t0) cc_final: 0.7979 (p0) REVERT: A 581 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 903 ARG cc_start: 0.6154 (mmm-85) cc_final: 0.5846 (mmm-85) REVERT: B 910 ASP cc_start: 0.5425 (t0) cc_final: 0.4829 (t0) REVERT: B 913 GLN cc_start: 0.5741 (pt0) cc_final: 0.5445 (pt0) REVERT: B 925 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 955 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7665 (ptmt) REVERT: B 1064 ARG cc_start: 0.6124 (mtm-85) cc_final: 0.5917 (mtm-85) REVERT: B 1175 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.6129 (mtm-85) REVERT: B 1219 GLN cc_start: 0.7711 (pt0) cc_final: 0.7261 (pt0) REVERT: B 1226 LYS cc_start: 0.7333 (pttm) cc_final: 0.6814 (ptmm) REVERT: B 1246 ASP cc_start: 0.7501 (p0) cc_final: 0.7160 (p0) outliers start: 20 outliers final: 6 residues processed: 153 average time/residue: 0.6034 time to fit residues: 97.6997 Evaluate side-chains 137 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 955 LYS Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1175 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 22 optimal weight: 0.4980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 378 HIS A 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.219073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138523 restraints weight = 8862.144| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.64 r_work: 0.3447 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8388 Z= 0.167 Angle : 0.598 11.499 11350 Z= 0.306 Chirality : 0.047 0.445 1244 Planarity : 0.003 0.027 1428 Dihedral : 5.870 54.442 1221 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.96 % Allowed : 12.74 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1006 helix: 1.92 (0.25), residues: 412 sheet: 0.33 (0.33), residues: 228 loop : -1.08 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 903 TYR 0.016 0.001 TYR A 306 PHE 0.016 0.001 PHE A 516 TRP 0.015 0.002 TRP B1266 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8383) covalent geometry : angle 0.57426 (11335) hydrogen bonds : bond 0.05498 ( 374) hydrogen bonds : angle 4.64696 ( 1077) link_BETA1-4 : bond 0.00652 ( 1) link_BETA1-4 : angle 0.84306 ( 3) link_BETA1-6 : bond 0.00630 ( 1) link_BETA1-6 : angle 1.15867 ( 3) link_NAG-ASN : bond 0.00554 ( 3) link_NAG-ASN : angle 5.92085 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7731 (tm-30) REVERT: A 197 MET cc_start: 0.6548 (mtm) cc_final: 0.5049 (tpt) REVERT: A 366 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6557 (mttm) REVERT: A 371 TRP cc_start: 0.7716 (t60) cc_final: 0.7470 (t60) REVERT: A 372 MET cc_start: 0.7363 (mtm) cc_final: 0.6852 (mmm) REVERT: A 379 ASP cc_start: 0.6176 (m-30) cc_final: 0.5899 (m-30) REVERT: A 444 ARG cc_start: 0.6887 (ttp-110) cc_final: 0.6442 (ttt180) REVERT: A 491 ARG cc_start: 0.7551 (tmt170) cc_final: 0.7058 (tpt-90) REVERT: A 497 PHE cc_start: 0.7955 (m-80) cc_final: 0.7565 (m-10) REVERT: A 522 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7413 (tppt) REVERT: A 563 GLU cc_start: 0.8096 (pt0) cc_final: 0.7455 (tp30) REVERT: A 567 VAL cc_start: 0.8493 (t) cc_final: 0.8056 (m) REVERT: A 568 ASN cc_start: 0.8230 (t0) cc_final: 0.7830 (p0) REVERT: A 581 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 742 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6668 (tm-30) REVERT: B 903 ARG cc_start: 0.6172 (mmm-85) cc_final: 0.5969 (mmm-85) REVERT: B 910 ASP cc_start: 0.5440 (t0) cc_final: 0.4615 (t0) REVERT: B 913 GLN cc_start: 0.5537 (pt0) cc_final: 0.5130 (pt0) REVERT: B 947 ILE cc_start: 0.7980 (tt) cc_final: 0.7662 (tp) REVERT: B 996 ARG cc_start: 0.6058 (mtp85) cc_final: 0.5741 (mtt180) REVERT: B 1061 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.5997 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6133 (mtm-85) cc_final: 0.5856 (mtm-85) REVERT: B 1097 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5960 (tt) REVERT: B 1175 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6019 (mtm-85) REVERT: B 1226 LYS cc_start: 0.7412 (pttm) cc_final: 0.6896 (ptmm) REVERT: B 1246 ASP cc_start: 0.7574 (p0) cc_final: 0.7258 (p0) outliers start: 26 outliers final: 11 residues processed: 154 average time/residue: 0.6302 time to fit residues: 102.6445 Evaluate side-chains 142 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.219969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137712 restraints weight = 8988.971| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.69 r_work: 0.3448 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8388 Z= 0.152 Angle : 0.579 9.153 11350 Z= 0.297 Chirality : 0.046 0.406 1244 Planarity : 0.003 0.051 1428 Dihedral : 5.649 53.108 1221 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 14.90 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.27), residues: 1006 helix: 1.94 (0.25), residues: 414 sheet: 0.31 (0.34), residues: 227 loop : -1.02 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.015 0.001 TYR A 306 PHE 0.017 0.001 PHE A 512 TRP 0.014 0.001 TRP B1266 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8383) covalent geometry : angle 0.56243 (11335) hydrogen bonds : bond 0.05169 ( 374) hydrogen bonds : angle 4.51659 ( 1077) link_BETA1-4 : bond 0.00786 ( 1) link_BETA1-4 : angle 0.97575 ( 3) link_BETA1-6 : bond 0.00696 ( 1) link_BETA1-6 : angle 1.31434 ( 3) link_NAG-ASN : bond 0.00464 ( 3) link_NAG-ASN : angle 4.86385 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6521 (mtm) cc_final: 0.5067 (tpt) REVERT: A 366 LYS cc_start: 0.7169 (mtmt) cc_final: 0.6509 (mttm) REVERT: A 371 TRP cc_start: 0.7736 (t60) cc_final: 0.7485 (t60) REVERT: A 372 MET cc_start: 0.7335 (mtm) cc_final: 0.6873 (mmp) REVERT: A 379 ASP cc_start: 0.6121 (m-30) cc_final: 0.5882 (m-30) REVERT: A 444 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.6261 (ttt180) REVERT: A 491 ARG cc_start: 0.7533 (tmt170) cc_final: 0.7029 (tpt-90) REVERT: A 497 PHE cc_start: 0.7946 (m-80) cc_final: 0.7579 (m-10) REVERT: A 522 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7443 (tppt) REVERT: A 563 GLU cc_start: 0.8117 (pt0) cc_final: 0.7497 (tp30) REVERT: A 567 VAL cc_start: 0.8474 (t) cc_final: 0.8243 (m) REVERT: A 581 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 742 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6704 (tm-30) REVERT: B 910 ASP cc_start: 0.5366 (t0) cc_final: 0.5047 (t0) REVERT: B 925 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 996 ARG cc_start: 0.6051 (mtp85) cc_final: 0.5705 (mtt180) REVERT: B 1061 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.5969 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6159 (mtm-85) cc_final: 0.5835 (mtm-85) REVERT: B 1106 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6212 (mp10) REVERT: B 1115 ASN cc_start: 0.7166 (m110) cc_final: 0.6833 (t0) REVERT: B 1175 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6051 (mtm-85) REVERT: B 1209 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5598 (pp) REVERT: B 1219 GLN cc_start: 0.7200 (pt0) cc_final: 0.6881 (pt0) REVERT: B 1226 LYS cc_start: 0.7465 (pttm) cc_final: 0.6871 (ptmm) REVERT: B 1246 ASP cc_start: 0.7640 (p0) cc_final: 0.7185 (p0) REVERT: B 1265 ASN cc_start: 0.7803 (m-40) cc_final: 0.7551 (m110) outliers start: 24 outliers final: 13 residues processed: 148 average time/residue: 0.6556 time to fit residues: 102.5414 Evaluate side-chains 142 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN B1199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.219155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138864 restraints weight = 8929.528| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.63 r_work: 0.3453 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8388 Z= 0.145 Angle : 0.565 9.664 11350 Z= 0.291 Chirality : 0.044 0.356 1244 Planarity : 0.003 0.034 1428 Dihedral : 5.432 50.297 1221 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.16 % Allowed : 16.84 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1006 helix: 2.01 (0.25), residues: 413 sheet: 0.35 (0.34), residues: 226 loop : -1.05 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.017 0.001 TYR B1133 PHE 0.015 0.001 PHE A 516 TRP 0.016 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8383) covalent geometry : angle 0.55323 (11335) hydrogen bonds : bond 0.05022 ( 374) hydrogen bonds : angle 4.47093 ( 1077) link_BETA1-4 : bond 0.00672 ( 1) link_BETA1-4 : angle 1.00741 ( 3) link_BETA1-6 : bond 0.00507 ( 1) link_BETA1-6 : angle 1.18569 ( 3) link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 4.07249 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6536 (mtm) cc_final: 0.5056 (tpt) REVERT: A 227 ASP cc_start: 0.8380 (m-30) cc_final: 0.7964 (m-30) REVERT: A 366 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6528 (mttm) REVERT: A 372 MET cc_start: 0.7355 (mtm) cc_final: 0.6874 (mmp) REVERT: A 444 ARG cc_start: 0.6735 (ttp-110) cc_final: 0.6267 (ttt180) REVERT: A 449 MET cc_start: 0.7464 (mtp) cc_final: 0.7249 (mtp) REVERT: A 491 ARG cc_start: 0.7532 (tmt170) cc_final: 0.6974 (tpt-90) REVERT: A 497 PHE cc_start: 0.7943 (m-80) cc_final: 0.7664 (m-10) REVERT: A 522 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7466 (tppt) REVERT: A 535 TYR cc_start: 0.8502 (t80) cc_final: 0.8250 (t80) REVERT: A 563 GLU cc_start: 0.8114 (pt0) cc_final: 0.7558 (tp30) REVERT: A 567 VAL cc_start: 0.8458 (t) cc_final: 0.8222 (m) REVERT: A 581 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 742 GLN cc_start: 0.6981 (tm-30) cc_final: 0.6667 (tm-30) REVERT: B 910 ASP cc_start: 0.5356 (t0) cc_final: 0.5017 (t0) REVERT: B 925 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 996 ARG cc_start: 0.6076 (mtp85) cc_final: 0.5735 (mtt180) REVERT: B 1061 ARG cc_start: 0.6732 (mtm-85) cc_final: 0.5985 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6179 (mtm-85) cc_final: 0.5862 (mtm-85) REVERT: B 1106 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6166 (mp10) REVERT: B 1115 ASN cc_start: 0.7224 (m110) cc_final: 0.6976 (t0) REVERT: B 1175 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6019 (mtm-85) REVERT: B 1209 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5594 (pp) REVERT: B 1224 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6761 (mmmt) REVERT: B 1226 LYS cc_start: 0.7454 (pttm) cc_final: 0.6871 (ptmm) REVERT: B 1246 ASP cc_start: 0.7575 (p0) cc_final: 0.7127 (p0) REVERT: B 1265 ASN cc_start: 0.7810 (m-40) cc_final: 0.7598 (m110) REVERT: B 1282 TRP cc_start: 0.7256 (m100) cc_final: 0.6749 (m100) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.6330 time to fit residues: 98.1944 Evaluate side-chains 141 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 742 GLN B 988 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.218478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137899 restraints weight = 8851.965| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.63 r_work: 0.3438 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8388 Z= 0.156 Angle : 0.566 10.597 11350 Z= 0.294 Chirality : 0.044 0.302 1244 Planarity : 0.003 0.031 1428 Dihedral : 5.240 46.975 1221 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.30 % Allowed : 16.61 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1006 helix: 2.01 (0.25), residues: 411 sheet: 0.27 (0.34), residues: 229 loop : -1.06 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 903 TYR 0.015 0.001 TYR A 306 PHE 0.018 0.001 PHE A 512 TRP 0.013 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8383) covalent geometry : angle 0.55716 (11335) hydrogen bonds : bond 0.05257 ( 374) hydrogen bonds : angle 4.47727 ( 1077) link_BETA1-4 : bond 0.00708 ( 1) link_BETA1-4 : angle 1.11083 ( 3) link_BETA1-6 : bond 0.00386 ( 1) link_BETA1-6 : angle 1.15900 ( 3) link_NAG-ASN : bond 0.00418 ( 3) link_NAG-ASN : angle 3.53050 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6428 (mtm) cc_final: 0.4970 (tpt) REVERT: A 366 LYS cc_start: 0.7201 (mtmt) cc_final: 0.6538 (mttm) REVERT: A 372 MET cc_start: 0.7429 (mtm) cc_final: 0.6939 (mmp) REVERT: A 444 ARG cc_start: 0.6871 (ttp-110) cc_final: 0.6375 (ttt180) REVERT: A 449 MET cc_start: 0.7604 (mtp) cc_final: 0.7399 (mtp) REVERT: A 491 ARG cc_start: 0.7520 (tmt170) cc_final: 0.6969 (tpt-90) REVERT: A 522 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7528 (tppt) REVERT: A 535 TYR cc_start: 0.8553 (t80) cc_final: 0.8282 (t80) REVERT: A 563 GLU cc_start: 0.8176 (pt0) cc_final: 0.7718 (tp30) REVERT: A 567 VAL cc_start: 0.8601 (t) cc_final: 0.8373 (m) REVERT: A 581 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7298 (mm-30) REVERT: B 910 ASP cc_start: 0.5318 (t0) cc_final: 0.5038 (t0) REVERT: B 925 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 996 ARG cc_start: 0.6109 (mtp85) cc_final: 0.5791 (mtt180) REVERT: B 1000 LYS cc_start: 0.7746 (tptp) cc_final: 0.7529 (tppp) REVERT: B 1061 ARG cc_start: 0.6738 (mtm-85) cc_final: 0.5987 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6257 (mtm-85) cc_final: 0.5912 (mtm-85) REVERT: B 1106 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: B 1175 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6165 (mtm-85) REVERT: B 1193 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6135 (mm) REVERT: B 1209 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5692 (pp) REVERT: B 1224 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6968 (mmmt) REVERT: B 1226 LYS cc_start: 0.7471 (pttm) cc_final: 0.6890 (ptmm) REVERT: B 1246 ASP cc_start: 0.7453 (p0) cc_final: 0.7016 (p0) REVERT: B 1265 ASN cc_start: 0.7851 (m-40) cc_final: 0.7618 (m110) REVERT: B 1282 TRP cc_start: 0.7300 (m100) cc_final: 0.6962 (m100) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 0.5964 time to fit residues: 94.2073 Evaluate side-chains 146 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 513 ASN A 578 HIS A 646 ASN B 988 GLN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.211421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130051 restraints weight = 9152.270| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.61 r_work: 0.3334 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.101 8388 Z= 0.456 Angle : 0.823 11.052 11350 Z= 0.431 Chirality : 0.056 0.394 1244 Planarity : 0.005 0.048 1428 Dihedral : 6.002 51.666 1221 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.10 % Allowed : 16.50 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.25), residues: 1006 helix: 0.79 (0.24), residues: 407 sheet: 0.16 (0.35), residues: 213 loop : -1.27 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 624 TYR 0.031 0.003 TYR A 306 PHE 0.024 0.003 PHE A 170 TRP 0.019 0.003 TRP A 467 HIS 0.006 0.002 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.01113 ( 8383) covalent geometry : angle 0.81259 (11335) hydrogen bonds : bond 0.08564 ( 374) hydrogen bonds : angle 5.25087 ( 1077) link_BETA1-4 : bond 0.00592 ( 1) link_BETA1-4 : angle 1.42072 ( 3) link_BETA1-6 : bond 0.00048 ( 1) link_BETA1-6 : angle 1.59754 ( 3) link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 4.68853 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6498 (mtm) cc_final: 0.4974 (tmm) REVERT: A 366 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7097 (mttm) REVERT: A 372 MET cc_start: 0.7645 (mtm) cc_final: 0.7192 (mmp) REVERT: A 444 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6668 (ttt180) REVERT: A 449 MET cc_start: 0.7713 (mtp) cc_final: 0.7488 (mtp) REVERT: A 491 ARG cc_start: 0.7446 (tmt170) cc_final: 0.7029 (tpt-90) REVERT: A 515 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7710 (ptpp) REVERT: A 522 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7567 (tppt) REVERT: A 563 GLU cc_start: 0.8311 (pt0) cc_final: 0.7888 (tp30) REVERT: A 568 ASN cc_start: 0.8452 (t0) cc_final: 0.8017 (p0) REVERT: A 570 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7118 (mtm110) REVERT: A 581 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 910 ASP cc_start: 0.5367 (t0) cc_final: 0.5109 (t0) REVERT: B 925 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 975 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7693 (ptmm) REVERT: B 982 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 996 ARG cc_start: 0.6117 (mtp85) cc_final: 0.5847 (mtt180) REVERT: B 1000 LYS cc_start: 0.8034 (tptp) cc_final: 0.7714 (tppp) REVERT: B 1061 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.5940 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6518 (mtm-85) cc_final: 0.6126 (mtm-85) REVERT: B 1089 ASP cc_start: 0.8659 (m-30) cc_final: 0.8299 (m-30) REVERT: B 1106 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: B 1111 TYR cc_start: 0.7344 (m-80) cc_final: 0.7082 (m-10) REVERT: B 1133 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5267 (p90) REVERT: B 1175 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6227 (mtm-85) REVERT: B 1224 LYS cc_start: 0.7238 (mmtt) cc_final: 0.7002 (mmmt) REVERT: B 1226 LYS cc_start: 0.7528 (pttm) cc_final: 0.6938 (ptmm) REVERT: B 1246 ASP cc_start: 0.7623 (p0) cc_final: 0.7367 (p0) REVERT: B 1265 ASN cc_start: 0.7874 (m-40) cc_final: 0.7667 (m110) outliers start: 36 outliers final: 15 residues processed: 157 average time/residue: 0.5830 time to fit residues: 96.8825 Evaluate side-chains 144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 TYR Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.217675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138084 restraints weight = 8926.652| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.54 r_work: 0.3438 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8388 Z= 0.164 Angle : 0.620 12.474 11350 Z= 0.319 Chirality : 0.045 0.335 1244 Planarity : 0.003 0.032 1428 Dihedral : 5.528 52.028 1221 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 18.66 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.26), residues: 1006 helix: 1.51 (0.25), residues: 410 sheet: 0.23 (0.34), residues: 224 loop : -1.24 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 903 TYR 0.019 0.001 TYR B1133 PHE 0.022 0.001 PHE A 512 TRP 0.019 0.002 TRP B1266 HIS 0.005 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8383) covalent geometry : angle 0.61217 (11335) hydrogen bonds : bond 0.05517 ( 374) hydrogen bonds : angle 4.72274 ( 1077) link_BETA1-4 : bond 0.00611 ( 1) link_BETA1-4 : angle 0.98083 ( 3) link_BETA1-6 : bond 0.00369 ( 1) link_BETA1-6 : angle 1.19780 ( 3) link_NAG-ASN : bond 0.00477 ( 3) link_NAG-ASN : angle 3.50028 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.7588 (ttm110) cc_final: 0.7203 (mtm110) REVERT: A 197 MET cc_start: 0.6558 (mtm) cc_final: 0.5003 (tmm) REVERT: A 366 LYS cc_start: 0.7380 (mtmt) cc_final: 0.6745 (mttm) REVERT: A 372 MET cc_start: 0.7553 (mtm) cc_final: 0.7085 (mmp) REVERT: A 444 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6470 (ttt180) REVERT: A 491 ARG cc_start: 0.7435 (tmt170) cc_final: 0.7014 (tpt-90) REVERT: A 522 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7547 (tppt) REVERT: A 563 GLU cc_start: 0.8188 (pt0) cc_final: 0.7727 (tp30) REVERT: A 567 VAL cc_start: 0.8789 (t) cc_final: 0.8523 (m) REVERT: A 581 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7343 (mm-30) REVERT: B 910 ASP cc_start: 0.5458 (t0) cc_final: 0.5161 (t0) REVERT: B 925 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 975 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7851 (ptmm) REVERT: B 982 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 996 ARG cc_start: 0.6061 (mtp85) cc_final: 0.5797 (mtt180) REVERT: B 1000 LYS cc_start: 0.7947 (tptp) cc_final: 0.7660 (tppp) REVERT: B 1061 ARG cc_start: 0.6669 (mtm-85) cc_final: 0.5874 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6427 (mtm-85) cc_final: 0.6052 (mtm-85) REVERT: B 1089 ASP cc_start: 0.8672 (m-30) cc_final: 0.8312 (m-30) REVERT: B 1175 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6330 (mtm-85) REVERT: B 1209 LEU cc_start: 0.6891 (mm) cc_final: 0.6244 (pp) REVERT: B 1224 LYS cc_start: 0.7174 (mmtt) cc_final: 0.6944 (mmmt) REVERT: B 1226 LYS cc_start: 0.7495 (pttm) cc_final: 0.6949 (ptmm) REVERT: B 1246 ASP cc_start: 0.7568 (p0) cc_final: 0.7124 (p0) REVERT: B 1265 ASN cc_start: 0.7915 (m-40) cc_final: 0.7658 (m110) outliers start: 24 outliers final: 13 residues processed: 147 average time/residue: 0.5904 time to fit residues: 91.8853 Evaluate side-chains 144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 578 HIS A 646 ASN B 988 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.217237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137522 restraints weight = 8983.264| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.55 r_work: 0.3429 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8388 Z= 0.179 Angle : 0.618 11.273 11350 Z= 0.320 Chirality : 0.045 0.328 1244 Planarity : 0.003 0.029 1428 Dihedral : 5.284 49.325 1221 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 19.34 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1006 helix: 1.65 (0.25), residues: 410 sheet: 0.15 (0.34), residues: 213 loop : -1.17 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 903 TYR 0.017 0.001 TYR B1133 PHE 0.013 0.001 PHE A 516 TRP 0.029 0.002 TRP B1282 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8383) covalent geometry : angle 0.61099 (11335) hydrogen bonds : bond 0.05692 ( 374) hydrogen bonds : angle 4.67491 ( 1077) link_BETA1-4 : bond 0.00565 ( 1) link_BETA1-4 : angle 1.12515 ( 3) link_BETA1-6 : bond 0.00355 ( 1) link_BETA1-6 : angle 1.20576 ( 3) link_NAG-ASN : bond 0.00461 ( 3) link_NAG-ASN : angle 3.29060 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7085 (mtm110) REVERT: A 197 MET cc_start: 0.6401 (mtm) cc_final: 0.4884 (tmm) REVERT: A 366 LYS cc_start: 0.7394 (mtmt) cc_final: 0.6757 (mttm) REVERT: A 372 MET cc_start: 0.7574 (mtm) cc_final: 0.7111 (mmp) REVERT: A 382 MET cc_start: 0.6969 (mmt) cc_final: 0.6634 (mpt) REVERT: A 444 ARG cc_start: 0.7020 (ttp-110) cc_final: 0.6462 (ttt180) REVERT: A 491 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7008 (tpt-90) REVERT: A 522 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7607 (tppt) REVERT: A 563 GLU cc_start: 0.8237 (pt0) cc_final: 0.7768 (tp30) REVERT: A 567 VAL cc_start: 0.8822 (t) cc_final: 0.8560 (m) REVERT: A 581 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 910 ASP cc_start: 0.5459 (t0) cc_final: 0.5223 (t0) REVERT: B 925 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7140 (mm-30) REVERT: B 975 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7785 (ptmm) REVERT: B 982 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 1000 LYS cc_start: 0.7864 (tptp) cc_final: 0.7597 (tppp) REVERT: B 1061 ARG cc_start: 0.6651 (mtm-85) cc_final: 0.5857 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6429 (mtm-85) cc_final: 0.6041 (mtm-85) REVERT: B 1089 ASP cc_start: 0.8654 (m-30) cc_final: 0.8296 (m-30) REVERT: B 1105 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7329 (tt) REVERT: B 1115 ASN cc_start: 0.7505 (m110) cc_final: 0.7129 (t0) REVERT: B 1175 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6261 (mtm-85) REVERT: B 1210 GLU cc_start: 0.7360 (tp30) cc_final: 0.7034 (tm-30) REVERT: B 1224 LYS cc_start: 0.7103 (mmtt) cc_final: 0.6864 (mmmt) REVERT: B 1226 LYS cc_start: 0.7455 (pttm) cc_final: 0.6932 (ptmm) REVERT: B 1246 ASP cc_start: 0.7516 (p0) cc_final: 0.7119 (p0) REVERT: B 1265 ASN cc_start: 0.7893 (m-40) cc_final: 0.7645 (m110) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.6597 time to fit residues: 100.0206 Evaluate side-chains 141 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1175 ARG Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 96 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.221621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143481 restraints weight = 8920.653| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.55 r_work: 0.3510 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8388 Z= 0.123 Angle : 0.576 11.893 11350 Z= 0.299 Chirality : 0.043 0.283 1244 Planarity : 0.003 0.038 1428 Dihedral : 4.849 46.315 1221 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.14 % Allowed : 20.82 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1006 helix: 1.99 (0.25), residues: 409 sheet: 0.19 (0.34), residues: 224 loop : -1.15 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 903 TYR 0.017 0.001 TYR B1133 PHE 0.023 0.001 PHE A 512 TRP 0.028 0.002 TRP B1282 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8383) covalent geometry : angle 0.57131 (11335) hydrogen bonds : bond 0.04407 ( 374) hydrogen bonds : angle 4.44174 ( 1077) link_BETA1-4 : bond 0.00585 ( 1) link_BETA1-4 : angle 1.24975 ( 3) link_BETA1-6 : bond 0.00452 ( 1) link_BETA1-6 : angle 1.17511 ( 3) link_NAG-ASN : bond 0.00476 ( 3) link_NAG-ASN : angle 2.54771 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.7745 (tp30) cc_final: 0.7274 (tp30) REVERT: A 157 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7030 (mtm110) REVERT: A 197 MET cc_start: 0.6340 (mtm) cc_final: 0.4871 (tmm) REVERT: A 366 LYS cc_start: 0.7200 (mtmt) cc_final: 0.6645 (mttm) REVERT: A 372 MET cc_start: 0.7534 (mtm) cc_final: 0.7037 (mmp) REVERT: A 382 MET cc_start: 0.6901 (mmt) cc_final: 0.6514 (mpt) REVERT: A 444 ARG cc_start: 0.6822 (ttp-110) cc_final: 0.6268 (ttt180) REVERT: A 491 ARG cc_start: 0.7420 (tmt170) cc_final: 0.7044 (tpt-90) REVERT: A 535 TYR cc_start: 0.8604 (t80) cc_final: 0.8278 (t80) REVERT: A 563 GLU cc_start: 0.8175 (pt0) cc_final: 0.7734 (tp30) REVERT: A 567 VAL cc_start: 0.8782 (t) cc_final: 0.8560 (m) REVERT: A 572 ILE cc_start: 0.8596 (mt) cc_final: 0.8269 (mp) REVERT: B 910 ASP cc_start: 0.5420 (t0) cc_final: 0.4952 (t0) REVERT: B 913 GLN cc_start: 0.5506 (pt0) cc_final: 0.5069 (pt0) REVERT: B 925 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7119 (mm-30) REVERT: B 982 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7152 (mt-10) REVERT: B 1000 LYS cc_start: 0.7827 (tptp) cc_final: 0.7582 (tppp) REVERT: B 1061 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.5904 (ptp-170) REVERT: B 1064 ARG cc_start: 0.6331 (mtm-85) cc_final: 0.5947 (mtm-85) REVERT: B 1175 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6243 (mtm-85) REVERT: B 1210 GLU cc_start: 0.7363 (tp30) cc_final: 0.7022 (tm-30) REVERT: B 1224 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6839 (mmmt) REVERT: B 1226 LYS cc_start: 0.7389 (pttm) cc_final: 0.6862 (ptmm) REVERT: B 1246 ASP cc_start: 0.7555 (p0) cc_final: 0.7149 (p0) outliers start: 10 outliers final: 6 residues processed: 128 average time/residue: 0.6635 time to fit residues: 89.6507 Evaluate side-chains 130 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1175 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.220304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141165 restraints weight = 8969.524| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.58 r_work: 0.3483 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8388 Z= 0.133 Angle : 0.578 11.537 11350 Z= 0.298 Chirality : 0.043 0.279 1244 Planarity : 0.003 0.031 1428 Dihedral : 4.682 44.722 1221 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.37 % Allowed : 20.93 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1006 helix: 2.07 (0.25), residues: 412 sheet: 0.21 (0.34), residues: 224 loop : -1.18 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 903 TYR 0.016 0.001 TYR B1133 PHE 0.012 0.001 PHE A 516 TRP 0.025 0.002 TRP B1282 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8383) covalent geometry : angle 0.57344 (11335) hydrogen bonds : bond 0.04674 ( 374) hydrogen bonds : angle 4.44890 ( 1077) link_BETA1-4 : bond 0.00689 ( 1) link_BETA1-4 : angle 1.34064 ( 3) link_BETA1-6 : bond 0.00459 ( 1) link_BETA1-6 : angle 1.17374 ( 3) link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 2.54033 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4411.02 seconds wall clock time: 75 minutes 44.03 seconds (4544.03 seconds total)