Starting phenix.real_space_refine on Sat Dec 28 09:58:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlc_36392/12_2024/8jlc_36392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlc_36392/12_2024/8jlc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlc_36392/12_2024/8jlc_36392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlc_36392/12_2024/8jlc_36392.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlc_36392/12_2024/8jlc_36392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlc_36392/12_2024/8jlc_36392.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.47, per 1000 atoms: 0.67 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: 2.40 Conformation dependent library (CDL) restraints added in 924.6 milliseconds 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: 0.87 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: 2.52 Time building geometry restraints manager: 2.67 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- 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 0.176 8383 Z= 0.703 Angle : 1.185 15.868 11335 Z= 0.775 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (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 TRP 0.085 0.012 TRP A 467 HIS 0.013 0.004 HIS A 161 PHE 0.068 0.011 PHE A 299 TYR 0.053 0.009 TYR A 169 ARG 0.024 0.003 ARG B1140 *********************** 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 : 0.925 Fit side-chains 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: 0.7946 (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 1203 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4936 (mm-30) 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: 0.6682 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.4024 time to fit residues: 260.8305 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 : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.0050 chunk 91 optimal weight: 0.2980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8383 Z= 0.189 Angle : 0.577 8.180 11335 Z= 0.306 Chirality : 0.046 0.473 1244 Planarity : 0.003 0.034 1428 Dihedral : 6.235 56.778 1221 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1006 helix: 1.95 (0.25), residues: 408 sheet: 0.12 (0.34), residues: 231 loop : -1.17 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 300 HIS 0.004 0.001 HIS A 378 PHE 0.017 0.001 PHE A 512 TYR 0.013 0.001 TYR A 306 ARG 0.005 0.001 ARG B 903 *********************** 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 : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6015 (tpp80) cc_final: 0.5714 (mtp85) REVERT: A 146 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7740 (tm-30) REVERT: A 197 MET cc_start: 0.6331 (mtm) cc_final: 0.5781 (ttm) REVERT: A 227 ASP cc_start: 0.7903 (m-30) cc_final: 0.7544 (m-30) REVERT: A 366 LYS cc_start: 0.6359 (mtmt) cc_final: 0.6105 (mttm) REVERT: A 372 MET cc_start: 0.7304 (mtm) cc_final: 0.6991 (mmm) REVERT: A 379 ASP cc_start: 0.5995 (m-30) cc_final: 0.5789 (m-30) REVERT: A 444 ARG cc_start: 0.6060 (ttp-110) cc_final: 0.5798 (ttt180) REVERT: A 491 ARG cc_start: 0.7414 (tmt170) cc_final: 0.7077 (tpt-90) REVERT: A 520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7532 (tpt170) REVERT: A 522 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7122 (tppt) REVERT: A 563 GLU cc_start: 0.8186 (pt0) cc_final: 0.7298 (tp30) REVERT: A 567 VAL cc_start: 0.7603 (t) cc_final: 0.7166 (m) REVERT: A 568 ASN cc_start: 0.8227 (t0) cc_final: 0.7874 (p0) REVERT: A 619 MET cc_start: 0.7372 (mmt) cc_final: 0.7100 (mmt) REVERT: B 903 ARG cc_start: 0.5860 (mmm-85) cc_final: 0.5650 (mmm-85) REVERT: B 910 ASP cc_start: 0.5190 (t0) cc_final: 0.4730 (t0) REVERT: B 1021 ASN cc_start: 0.6870 (m-40) cc_final: 0.6516 (m-40) REVERT: B 1219 GLN cc_start: 0.7277 (pt0) cc_final: 0.6947 (pt0) REVERT: B 1226 LYS cc_start: 0.6829 (pttm) cc_final: 0.6562 (ptmm) REVERT: B 1246 ASP cc_start: 0.7223 (p0) cc_final: 0.6925 (p0) outliers start: 20 outliers final: 6 residues processed: 153 average time/residue: 1.2757 time to fit residues: 207.5175 Evaluate side-chains 135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 1019 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 A 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8383 Z= 0.385 Angle : 0.643 8.311 11335 Z= 0.338 Chirality : 0.050 0.449 1244 Planarity : 0.004 0.036 1428 Dihedral : 6.101 58.480 1221 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.53 % Allowed : 12.51 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1006 helix: 1.53 (0.25), residues: 411 sheet: 0.28 (0.34), residues: 227 loop : -1.17 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 985 HIS 0.005 0.002 HIS A 387 PHE 0.018 0.002 PHE A 640 TYR 0.021 0.002 TYR A 306 ARG 0.004 0.001 ARG B 903 *********************** 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 169 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5911 (tpp80) cc_final: 0.5627 (mtp85) REVERT: A 146 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7704 (tm-30) REVERT: A 197 MET cc_start: 0.6223 (mtm) cc_final: 0.5087 (tpt) REVERT: A 301 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7716 (ttp) REVERT: A 366 LYS cc_start: 0.6504 (mtmt) cc_final: 0.6241 (mttm) REVERT: A 372 MET cc_start: 0.7159 (mtm) cc_final: 0.6945 (mmm) REVERT: A 444 ARG cc_start: 0.6093 (ttp-110) cc_final: 0.5674 (ttt180) REVERT: A 491 ARG cc_start: 0.7420 (tmt170) cc_final: 0.6964 (tpt-90) REVERT: A 520 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7369 (tpt170) REVERT: A 522 LYS cc_start: 0.7338 (ttpt) cc_final: 0.7125 (tppt) REVERT: A 563 GLU cc_start: 0.8247 (pt0) cc_final: 0.7422 (tp30) REVERT: A 567 VAL cc_start: 0.7678 (t) cc_final: 0.7416 (m) REVERT: A 742 GLN cc_start: 0.7101 (tm-30) cc_final: 0.6749 (tm-30) REVERT: B 1061 ARG cc_start: 0.6308 (mtm-85) cc_final: 0.5949 (ptp-170) REVERT: B 1097 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5844 (tt) REVERT: B 1226 LYS cc_start: 0.6848 (pttm) cc_final: 0.6605 (ptmm) REVERT: B 1246 ASP cc_start: 0.7295 (p0) cc_final: 0.6950 (p0) outliers start: 31 outliers final: 13 residues processed: 157 average time/residue: 1.2637 time to fit residues: 210.6565 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 : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 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 661 VAL 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 944 SER 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 1289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.0020 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN B1265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8383 Z= 0.169 Angle : 0.556 7.721 11335 Z= 0.289 Chirality : 0.045 0.417 1244 Planarity : 0.003 0.030 1428 Dihedral : 5.770 58.360 1221 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.16 % Allowed : 16.50 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1006 helix: 1.93 (0.25), residues: 414 sheet: 0.30 (0.34), residues: 227 loop : -1.06 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.018 0.001 PHE A 512 TYR 0.016 0.001 TYR B1111 ARG 0.006 0.000 ARG A 141 *********************** 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 156 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5971 (tpp80) cc_final: 0.5625 (mtp85) REVERT: A 146 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7724 (tm-30) REVERT: A 197 MET cc_start: 0.6252 (mtm) cc_final: 0.5706 (ttm) REVERT: A 227 ASP cc_start: 0.8015 (m-30) cc_final: 0.7443 (m-30) REVERT: A 301 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: A 366 LYS cc_start: 0.6253 (mtmt) cc_final: 0.6026 (mttm) REVERT: A 372 MET cc_start: 0.7252 (mtm) cc_final: 0.6990 (mmp) REVERT: A 444 ARG cc_start: 0.5872 (ttp-110) cc_final: 0.5540 (ttt180) REVERT: A 449 MET cc_start: 0.7051 (mtp) cc_final: 0.6766 (mtp) REVERT: A 491 ARG cc_start: 0.7379 (tmt170) cc_final: 0.6890 (tpt-90) REVERT: A 520 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7377 (tpt170) REVERT: A 522 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7166 (tppt) REVERT: A 563 GLU cc_start: 0.8205 (pt0) cc_final: 0.7380 (tp30) REVERT: A 567 VAL cc_start: 0.7640 (t) cc_final: 0.7390 (m) REVERT: A 619 MET cc_start: 0.7194 (mmt) cc_final: 0.6839 (tpt) REVERT: A 742 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6698 (tm-30) REVERT: B 947 ILE cc_start: 0.8015 (tt) cc_final: 0.7706 (tp) REVERT: B 1061 ARG cc_start: 0.6346 (mtm-85) cc_final: 0.5937 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6146 (mp10) REVERT: B 1115 ASN cc_start: 0.7313 (m110) cc_final: 0.6722 (t0) REVERT: B 1133 TYR cc_start: 0.4623 (p90) cc_final: 0.4302 (p90) REVERT: B 1209 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5230 (pp) REVERT: B 1226 LYS cc_start: 0.6877 (pttm) cc_final: 0.6602 (ptmm) REVERT: B 1246 ASP cc_start: 0.7351 (p0) cc_final: 0.7099 (p0) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 1.2808 time to fit residues: 199.9132 Evaluate side-chains 146 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 522 LYS 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 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 975 LYS 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 1209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8383 Z= 0.259 Angle : 0.579 9.671 11335 Z= 0.302 Chirality : 0.046 0.360 1244 Planarity : 0.004 0.065 1428 Dihedral : 5.678 59.915 1221 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.84 % Allowed : 17.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1006 helix: 1.83 (0.25), residues: 413 sheet: 0.23 (0.34), residues: 229 loop : -1.07 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.015 0.001 PHE A 516 TYR 0.017 0.001 TYR A 306 ARG 0.010 0.001 ARG A 141 *********************** 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 155 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5964 (tpp80) cc_final: 0.5584 (mtp85) REVERT: A 146 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7688 (tm-30) REVERT: A 197 MET cc_start: 0.6184 (mtm) cc_final: 0.5006 (tpt) REVERT: A 301 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7717 (ttp) REVERT: A 366 LYS cc_start: 0.6324 (mtmt) cc_final: 0.6088 (mttm) REVERT: A 372 MET cc_start: 0.7231 (mtm) cc_final: 0.6971 (mmp) REVERT: A 444 ARG cc_start: 0.5944 (ttp-110) cc_final: 0.5571 (ttt180) REVERT: A 449 MET cc_start: 0.7203 (mtp) cc_final: 0.6908 (mtp) REVERT: A 491 ARG cc_start: 0.7359 (tmt170) cc_final: 0.6947 (tpt-90) REVERT: A 520 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7453 (tpt170) REVERT: A 522 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7156 (tppt) REVERT: A 563 GLU cc_start: 0.8247 (pt0) cc_final: 0.7512 (tp30) REVERT: A 567 VAL cc_start: 0.7729 (t) cc_final: 0.7467 (m) REVERT: A 619 MET cc_start: 0.7232 (mmt) cc_final: 0.6917 (tpt) REVERT: A 742 GLN cc_start: 0.6946 (tm-30) cc_final: 0.6608 (tm-30) REVERT: B 1061 ARG cc_start: 0.6325 (mtm-85) cc_final: 0.5935 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6377 (mp10) REVERT: B 1133 TYR cc_start: 0.4664 (p90) cc_final: 0.4255 (p90) REVERT: B 1175 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.4121 (mtm-85) REVERT: B 1209 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5266 (pp) REVERT: B 1226 LYS cc_start: 0.6880 (pttm) cc_final: 0.6610 (ptmm) REVERT: B 1282 TRP cc_start: 0.7228 (m100) cc_final: 0.6717 (m100) outliers start: 25 outliers final: 12 residues processed: 142 average time/residue: 1.3254 time to fit residues: 199.5040 Evaluate side-chains 144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET 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 522 LYS 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 B residue 914 ILE Chi-restraints excluded: chain B residue 975 LYS 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 87 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 B 988 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8383 Z= 0.208 Angle : 0.548 10.736 11335 Z= 0.285 Chirality : 0.044 0.321 1244 Planarity : 0.003 0.055 1428 Dihedral : 5.461 56.627 1221 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.75 % Allowed : 16.27 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1006 helix: 1.97 (0.25), residues: 413 sheet: 0.24 (0.34), residues: 229 loop : -1.06 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.003 0.001 HIS A 494 PHE 0.016 0.001 PHE A 512 TYR 0.015 0.001 TYR B1111 ARG 0.009 0.000 ARG A 141 *********************** 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 160 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5962 (tpp80) cc_final: 0.5569 (mtp85) REVERT: A 146 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7710 (tm-30) REVERT: A 197 MET cc_start: 0.6048 (mtm) cc_final: 0.4891 (tpt) REVERT: A 227 ASP cc_start: 0.8182 (m-30) cc_final: 0.7881 (m-30) REVERT: A 301 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7699 (ttp) REVERT: A 366 LYS cc_start: 0.6215 (mtmt) cc_final: 0.6006 (mttm) REVERT: A 372 MET cc_start: 0.7258 (mtm) cc_final: 0.6993 (mmp) REVERT: A 444 ARG cc_start: 0.5823 (ttp-110) cc_final: 0.5395 (ttt180) REVERT: A 449 MET cc_start: 0.7171 (mtp) cc_final: 0.6923 (mtp) REVERT: A 491 ARG cc_start: 0.7355 (tmt170) cc_final: 0.6649 (tpt-90) REVERT: A 493 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: A 520 ARG cc_start: 0.7951 (mtt90) cc_final: 0.7446 (tpt170) REVERT: A 535 TYR cc_start: 0.8057 (t80) cc_final: 0.7842 (t80) REVERT: A 563 GLU cc_start: 0.8242 (pt0) cc_final: 0.7501 (tp30) REVERT: A 567 VAL cc_start: 0.7763 (t) cc_final: 0.7506 (m) REVERT: A 619 MET cc_start: 0.7222 (mmt) cc_final: 0.6864 (tpt) REVERT: A 742 GLN cc_start: 0.6983 (tm-30) cc_final: 0.6673 (tm-30) REVERT: B 1061 ARG cc_start: 0.6263 (mtm-85) cc_final: 0.5879 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6315 (mp10) REVERT: B 1133 TYR cc_start: 0.4812 (p90) cc_final: 0.4399 (p90) REVERT: B 1175 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4158 (mtm-85) REVERT: B 1209 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5328 (pp) outliers start: 33 outliers final: 11 residues processed: 146 average time/residue: 1.2559 time to fit residues: 195.4700 Evaluate side-chains 139 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 588 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 0.0050 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 988 GLN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8383 Z= 0.170 Angle : 0.545 11.256 11335 Z= 0.283 Chirality : 0.044 0.289 1244 Planarity : 0.003 0.047 1428 Dihedral : 5.270 53.273 1221 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.84 % Allowed : 17.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1006 helix: 2.04 (0.25), residues: 416 sheet: 0.22 (0.34), residues: 228 loop : -1.09 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.010 0.001 PHE A 516 TYR 0.013 0.001 TYR B1111 ARG 0.010 0.000 ARG A 141 *********************** 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 152 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5960 (tpp80) cc_final: 0.5607 (mtp85) REVERT: A 146 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7722 (tm-30) REVERT: A 197 MET cc_start: 0.6051 (mtm) cc_final: 0.4872 (tmm) REVERT: A 227 ASP cc_start: 0.8103 (m-30) cc_final: 0.7587 (m-30) REVERT: A 301 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7630 (ttp) REVERT: A 366 LYS cc_start: 0.6074 (mtmt) cc_final: 0.5842 (mttm) REVERT: A 372 MET cc_start: 0.7257 (mtm) cc_final: 0.6997 (mmp) REVERT: A 444 ARG cc_start: 0.5736 (ttp-110) cc_final: 0.5412 (ttt180) REVERT: A 449 MET cc_start: 0.7194 (mtp) cc_final: 0.6963 (mtp) REVERT: A 491 ARG cc_start: 0.7371 (tmt170) cc_final: 0.6635 (tpt-90) REVERT: A 493 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: A 520 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7444 (tpt170) REVERT: A 535 TYR cc_start: 0.8076 (t80) cc_final: 0.7875 (t80) REVERT: A 563 GLU cc_start: 0.8235 (pt0) cc_final: 0.7472 (tp30) REVERT: A 567 VAL cc_start: 0.7750 (t) cc_final: 0.7510 (m) REVERT: A 619 MET cc_start: 0.7163 (mmt) cc_final: 0.6881 (tpt) REVERT: A 627 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7231 (mmm) REVERT: A 742 GLN cc_start: 0.6998 (tm-30) cc_final: 0.6704 (tm-30) REVERT: B 1061 ARG cc_start: 0.6273 (mtm-85) cc_final: 0.5877 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6254 (mp10) REVERT: B 1133 TYR cc_start: 0.4896 (p90) cc_final: 0.4496 (p90) REVERT: B 1219 GLN cc_start: 0.6783 (pt0) cc_final: 0.5933 (pp30) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 1.3338 time to fit residues: 199.2675 Evaluate side-chains 140 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET 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 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 655 LEU 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 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8383 Z= 0.270 Angle : 0.597 11.880 11335 Z= 0.311 Chirality : 0.046 0.291 1244 Planarity : 0.003 0.052 1428 Dihedral : 5.207 45.672 1221 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.07 % Allowed : 18.77 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1006 helix: 1.84 (0.25), residues: 415 sheet: 0.19 (0.34), residues: 228 loop : -1.10 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1266 HIS 0.004 0.001 HIS A 494 PHE 0.018 0.001 PHE A 512 TYR 0.017 0.001 TYR A 306 ARG 0.013 0.001 ARG A 141 *********************** 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 151 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5983 (tpp80) cc_final: 0.5623 (mtp85) REVERT: A 146 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7679 (tm-30) REVERT: A 197 MET cc_start: 0.5998 (mtm) cc_final: 0.4824 (tmm) REVERT: A 301 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7691 (ttp) REVERT: A 366 LYS cc_start: 0.6233 (mtmt) cc_final: 0.5945 (mttm) REVERT: A 372 MET cc_start: 0.7243 (mtm) cc_final: 0.6967 (mmp) REVERT: A 379 ASP cc_start: 0.6213 (m-30) cc_final: 0.6002 (p0) REVERT: A 444 ARG cc_start: 0.5905 (ttp-110) cc_final: 0.5536 (ttt180) REVERT: A 449 MET cc_start: 0.7242 (mtp) cc_final: 0.7004 (mtp) REVERT: A 491 ARG cc_start: 0.7395 (tmt170) cc_final: 0.6755 (tpt-90) REVERT: A 493 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6902 (pt0) REVERT: A 520 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7425 (tpt170) REVERT: A 535 TYR cc_start: 0.8088 (t80) cc_final: 0.7876 (t80) REVERT: A 563 GLU cc_start: 0.8249 (pt0) cc_final: 0.7499 (tp30) REVERT: A 567 VAL cc_start: 0.7829 (t) cc_final: 0.7565 (m) REVERT: A 619 MET cc_start: 0.7155 (mmt) cc_final: 0.6812 (tpt) REVERT: A 742 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6738 (tm-30) REVERT: B 1061 ARG cc_start: 0.6277 (mtm-85) cc_final: 0.5878 (ptp-170) REVERT: B 1105 LEU cc_start: 0.7420 (tp) cc_final: 0.7119 (mt) REVERT: B 1106 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6367 (mp10) REVERT: B 1133 TYR cc_start: 0.5033 (p90) cc_final: 0.4569 (p90) REVERT: B 1175 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.4425 (mtm-85) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 1.2557 time to fit residues: 186.7134 Evaluate side-chains 140 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET 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 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU 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 975 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8383 Z= 0.197 Angle : 0.571 11.823 11335 Z= 0.296 Chirality : 0.044 0.280 1244 Planarity : 0.003 0.055 1428 Dihedral : 4.977 45.350 1221 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 18.89 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1006 helix: 1.96 (0.25), residues: 414 sheet: 0.17 (0.34), residues: 230 loop : -1.09 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1266 HIS 0.004 0.001 HIS A 494 PHE 0.013 0.001 PHE B1252 TYR 0.013 0.001 TYR A 306 ARG 0.014 0.000 ARG A 141 *********************** 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 146 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5951 (tpp80) cc_final: 0.5537 (mtp85) REVERT: A 146 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7699 (tm-30) REVERT: A 197 MET cc_start: 0.5923 (mtm) cc_final: 0.4760 (tmm) REVERT: A 227 ASP cc_start: 0.8112 (m-30) cc_final: 0.7615 (m-30) REVERT: A 301 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7681 (ttp) REVERT: A 372 MET cc_start: 0.7268 (mtm) cc_final: 0.7003 (mmp) REVERT: A 382 MET cc_start: 0.6087 (mmt) cc_final: 0.5873 (mpt) REVERT: A 444 ARG cc_start: 0.5801 (ttp-110) cc_final: 0.5435 (ttt180) REVERT: A 491 ARG cc_start: 0.7394 (tmt170) cc_final: 0.6761 (tpt-90) REVERT: A 493 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6831 (pt0) REVERT: A 520 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7429 (tpt170) REVERT: A 535 TYR cc_start: 0.8087 (t80) cc_final: 0.7878 (t80) REVERT: A 563 GLU cc_start: 0.8235 (pt0) cc_final: 0.7495 (tp30) REVERT: A 567 VAL cc_start: 0.7815 (t) cc_final: 0.7568 (m) REVERT: A 619 MET cc_start: 0.7158 (mmt) cc_final: 0.6909 (tpt) REVERT: A 742 GLN cc_start: 0.7100 (tm-30) cc_final: 0.6798 (tm-30) REVERT: B 1061 ARG cc_start: 0.6245 (mtm-85) cc_final: 0.5834 (ptp-170) REVERT: B 1105 LEU cc_start: 0.7426 (tp) cc_final: 0.6876 (mp) REVERT: B 1106 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6379 (mp10) REVERT: B 1133 TYR cc_start: 0.5120 (p90) cc_final: 0.4643 (p90) REVERT: B 1175 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.4557 (mtm-85) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 1.2762 time to fit residues: 186.0170 Evaluate side-chains 139 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET 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 493 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU 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 1074 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8383 Z= 0.310 Angle : 0.622 11.612 11335 Z= 0.324 Chirality : 0.046 0.300 1244 Planarity : 0.004 0.059 1428 Dihedral : 4.973 46.253 1221 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 19.23 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1006 helix: 1.76 (0.25), residues: 411 sheet: 0.07 (0.34), residues: 228 loop : -1.11 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 985 HIS 0.003 0.001 HIS A 494 PHE 0.018 0.002 PHE A 516 TYR 0.019 0.002 TYR A 306 ARG 0.017 0.001 ARG A 141 ********************** 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 146 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6034 (tpp80) cc_final: 0.5546 (mtp85) REVERT: A 146 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7668 (tm-30) REVERT: A 197 MET cc_start: 0.5911 (mtm) cc_final: 0.4801 (tmm) REVERT: A 301 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7710 (ttp) REVERT: A 372 MET cc_start: 0.7275 (mtm) cc_final: 0.7015 (mmp) REVERT: A 444 ARG cc_start: 0.5851 (ttp-110) cc_final: 0.5481 (ttt180) REVERT: A 491 ARG cc_start: 0.7389 (tmt170) cc_final: 0.6693 (tpt-90) REVERT: A 493 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: A 520 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7457 (tpt170) REVERT: A 563 GLU cc_start: 0.8259 (pt0) cc_final: 0.7549 (tp30) REVERT: A 567 VAL cc_start: 0.7836 (t) cc_final: 0.7567 (m) REVERT: A 619 MET cc_start: 0.7265 (mmt) cc_final: 0.6893 (tpt) REVERT: A 742 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6845 (tm-30) REVERT: B 1061 ARG cc_start: 0.6263 (mtm-85) cc_final: 0.5845 (ptp-170) REVERT: B 1105 LEU cc_start: 0.7532 (tp) cc_final: 0.7008 (mp) REVERT: B 1106 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: B 1133 TYR cc_start: 0.5143 (p90) cc_final: 0.4637 (p90) REVERT: B 1175 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5391 (mtm-85) outliers start: 25 outliers final: 13 residues processed: 137 average time/residue: 1.2040 time to fit residues: 175.4849 Evaluate side-chains 135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET 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 493 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU 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 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 chunk 70 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.221826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142791 restraints weight = 8825.309| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.57 r_work: 0.3507 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.166 Angle : 0.568 11.849 11335 Z= 0.296 Chirality : 0.043 0.276 1244 Planarity : 0.003 0.040 1428 Dihedral : 4.692 45.038 1221 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.16 % Allowed : 20.25 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1006 helix: 1.99 (0.25), residues: 415 sheet: 0.11 (0.34), residues: 230 loop : -1.09 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1266 HIS 0.004 0.001 HIS A 494 PHE 0.012 0.001 PHE A 516 TYR 0.012 0.001 TYR A 169 ARG 0.009 0.000 ARG B 903 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3814.56 seconds wall clock time: 68 minutes 54.34 seconds (4134.34 seconds total)