Starting phenix.real_space_refine on Thu Aug 6 11:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opt_17087/08_2026/8opt_17087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opt_17087/08_2026/8opt_17087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2026/8opt_17087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2026/8opt_17087.map" model { file = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2026/8opt_17087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2026/8opt_17087.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 36 5.16 5 C 4781 2.51 5 N 1338 2.21 5 O 1563 1.98 5 H 7197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14971 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 12651 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 43, 'TRANS': 739} Chain breaks: 7 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1740 Classifications: {'RNA': 54} Modifications used: {'3*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 26, 'rna3p_pyr': 18} Link IDs: {'rna2p': 10, 'rna3p': 43} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 578 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7018 SG CYS A 965 30.740 58.816 80.274 1.00 76.39 S ATOM 7058 SG CYS A 968 32.244 56.154 82.639 1.00 79.01 S ATOM 7229 SG CYS A 978 28.562 56.027 81.831 1.00 71.28 S ATOM 14423 SG CYS B 139 45.794 36.750 28.084 1.00101.21 S ATOM 14468 SG CYS B 142 49.793 36.545 27.527 1.00103.47 S ATOM 14591 SG CYS B 152 48.043 36.623 31.187 1.00 98.61 S Time building chain proxies: 2.52, per 1000 atoms: 0.17 Number of scatterers: 14971 At special positions: 0 Unit cell: (81.084, 114.636, 142.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 54 15.00 O 1563 8.00 N 1338 7.00 C 4781 6.00 H 7197 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 621 " distance=2.04 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 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 435.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" ND1 HIS A 973 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 978 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 968 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 965 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 152 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 139 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 142 " Number of angles added : 3 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 44.2% alpha, 9.8% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.673A pdb=" N LYS A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.752A pdb=" N LYS A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.814A pdb=" N LEU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.713A pdb=" N LEU A 464 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.890A pdb=" N GLY A 495 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 611 through 630 Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 994 through 1013 Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 4.213A pdb=" N ASP A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1090 removed outlier: 3.591A pdb=" N LYS A1089 " --> pdb=" O ARG A1085 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1141 removed outlier: 4.373A pdb=" N ASP A1141 " --> pdb=" O TYR A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1158 removed outlier: 4.028A pdb=" N LYS A1145 " --> pdb=" O ASP A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1183 Processing helix chain 'A' and resid 1219 through 1224 removed outlier: 3.731A pdb=" N TYR A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1247 Processing helix chain 'A' and resid 1266 through 1270 Processing helix chain 'A' and resid 1293 through 1311 Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.780A pdb=" N PHE A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339 removed outlier: 4.555A pdb=" N ASN A 354 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 353 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER A 410 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A 355 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 399 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP A 384 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 503 removed outlier: 5.455A pdb=" N LEU A 499 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU A 510 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 597 removed outlier: 4.492A pdb=" N ASP A 597 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1045 removed outlier: 3.844A pdb=" N ASP A1060 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A1059 " --> pdb=" O ASP A1119 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N SER A1121 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A1061 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE A1110 " --> pdb=" O ASN A1095 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASN A1095 " --> pdb=" O PHE A1110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1205 through 1206 removed outlier: 3.677A pdb=" N TRP A1209 " --> pdb=" O VAL A1206 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7179 1.03 - 1.23: 55 1.23 - 1.43: 3475 1.43 - 1.62: 4502 1.62 - 1.82: 46 Bond restraints: 15257 Sorted by residual: bond pdb=" N9 G D 45 " pdb=" C4 G D 45 " ideal model delta sigma weight residual 1.375 1.386 -0.011 8.00e-03 1.56e+04 1.85e+00 bond pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.90e-01 bond pdb=" CA ARG A1184 " pdb=" CB ARG A1184 " ideal model delta sigma weight residual 1.533 1.519 0.014 1.66e-02 3.63e+03 7.17e-01 bond pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.93e-01 bond pdb=" C GLN A1183 " pdb=" N ARG A1184 " ideal model delta sigma weight residual 1.331 1.341 -0.010 1.24e-02 6.50e+03 6.77e-01 ... (remaining 15252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 27160 1.78 - 3.57: 426 3.57 - 5.35: 19 5.35 - 7.14: 1 7.14 - 8.92: 1 Bond angle restraints: 27607 Sorted by residual: angle pdb=" O5' G D 53 " pdb=" C5' G D 53 " pdb=" C4' G D 53 " ideal model delta sigma weight residual 109.40 112.53 -3.13 8.00e-01 1.56e+00 1.53e+01 angle pdb=" O5' A D 19 " pdb=" C5' A D 19 " pdb=" C4' A D 19 " ideal model delta sigma weight residual 109.40 112.16 -2.76 8.00e-01 1.56e+00 1.19e+01 angle pdb=" O5' G D 65 " pdb=" C5' G D 65 " pdb=" C4' G D 65 " ideal model delta sigma weight residual 109.40 112.06 -2.66 8.00e-01 1.56e+00 1.11e+01 angle pdb=" O5' A D 30 " pdb=" C5' A D 30 " pdb=" C4' A D 30 " ideal model delta sigma weight residual 109.40 112.01 -2.61 8.00e-01 1.56e+00 1.07e+01 angle pdb=" O5' G D 20 " pdb=" C5' G D 20 " pdb=" C4' G D 20 " ideal model delta sigma weight residual 109.40 111.94 -2.54 8.00e-01 1.56e+00 1.01e+01 ... (remaining 27602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 6598 25.09 - 50.18: 475 50.18 - 75.27: 151 75.27 - 100.35: 12 100.35 - 125.44: 3 Dihedral angle restraints: 7239 sinusoidal: 4355 harmonic: 2884 Sorted by residual: dihedral pdb=" C4' C D 48 " pdb=" C3' C D 48 " pdb=" O3' C D 48 " pdb=" P A D 49 " ideal model delta sinusoidal sigma weight residual -110.00 10.20 -120.20 1 3.50e+01 8.16e-04 1.18e+01 dihedral pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " pdb=" CG ASP A 587 " pdb=" OD1 ASP A 587 " ideal model delta sinusoidal sigma weight residual -30.00 -88.33 58.33 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" O4' G D 45 " pdb=" C1' G D 45 " pdb=" N9 G D 45 " pdb=" C4 G D 45 " ideal model delta sinusoidal sigma weight residual 68.00 115.46 -47.46 1 1.70e+01 3.46e-03 1.08e+01 ... (remaining 7236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 836 0.026 - 0.051: 259 0.051 - 0.077: 73 0.077 - 0.103: 81 0.103 - 0.129: 50 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA VAL A 393 " pdb=" N VAL A 393 " pdb=" C VAL A 393 " pdb=" CB VAL A 393 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE A1204 " pdb=" N ILE A1204 " pdb=" C ILE A1204 " pdb=" CB ILE A1204 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1296 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A1207 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CG ASP A1207 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP A1207 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A1207 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1207 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ASP A1207 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A1207 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A1208 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1013 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A1014 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1014 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1014 " -0.021 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.81: 25 1.81 - 2.51: 11068 2.51 - 3.21: 45244 3.21 - 3.90: 57311 3.90 - 4.60: 87927 Nonbonded interactions: 201575 Sorted by model distance: nonbonded pdb=" HE1 HIS A 973 " pdb="ZN ZN A1501 " model vdw 1.116 1.408 nonbonded pdb=" OE1 GLU A1219 " pdb=" H GLU A1219 " model vdw 1.613 2.450 nonbonded pdb=" OD1 ASN A 567 " pdb=" H ASP A 570 " model vdw 1.620 2.450 nonbonded pdb=" O LEU A 214 " pdb="HE21 GLN A 218 " model vdw 1.628 2.450 nonbonded pdb=" HZ2 LYS A 976 " pdb=" OD1 ASP A 977 " model vdw 1.633 2.450 ... (remaining 201570 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 group one per residue 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: 3.960 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: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.010 Find NCS groups from input model: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.002 0.031 8068 Z= 0.112 Angle : 0.532 8.923 11174 Z= 0.344 Chirality : 0.040 0.129 1299 Planarity : 0.003 0.037 1217 Dihedral : 19.509 125.444 3359 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.14 % Allowed : 19.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.30), residues: 807 helix: 2.97 (0.28), residues: 337 sheet: 0.08 (0.56), residues: 86 loop : 0.04 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 970 TYR 0.010 0.001 TYR A1245 PHE 0.007 0.001 PHE A 955 TRP 0.005 0.001 TRP A 555 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 8060) covalent geometry : angle 0.53093 / 0.34 (11169) SS BOND : bond 0.00464 / 0.31 ( 1) SS BOND : angle 0.86277 / 0.58 ( 2) hydrogen bonds : bond 0.12020 / 8.29 ( 312) hydrogen bonds : angle 5.09320 / 3.96 ( 885) metal coordination : bond 0.00541 / 0.28 ( 7) metal coordination : angle 1.87773 / 1.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.1811 time to fit residues: 26.7961 Evaluate side-chains 108 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 ASN A1193 GLN B 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.217151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.184969 restraints weight = 40209.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.189700 restraints weight = 18433.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.192657 restraints weight = 10958.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.194552 restraints weight = 7884.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.195458 restraints weight = 6438.361| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8068 Z= 0.192 Angle : 0.545 6.324 11174 Z= 0.289 Chirality : 0.039 0.176 1299 Planarity : 0.004 0.044 1217 Dihedral : 18.911 121.855 1711 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.95 % Allowed : 18.59 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 807 helix: 2.46 (0.28), residues: 341 sheet: -0.26 (0.54), residues: 86 loop : -0.17 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.012 0.002 TYR A 562 PHE 0.016 0.001 PHE A1154 TRP 0.007 0.001 TRP A 555 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 8060) covalent geometry : angle 0.54169 / 0.29 (11169) SS BOND : bond 0.00807 / 0.54 ( 1) SS BOND : angle 1.45639 / 0.82 ( 2) hydrogen bonds : bond 0.04962 / 3.30 ( 312) hydrogen bonds : angle 4.73658 / 3.64 ( 885) metal coordination : bond 0.00718 / 0.40 ( 7) metal coordination : angle 3.71647 / 2.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7217 (tm-30) cc_final: 0.7009 (tm-30) REVERT: A 1141 ASP cc_start: 0.5751 (OUTLIER) cc_final: 0.4107 (m-30) outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 0.1752 time to fit residues: 28.8472 Evaluate side-chains 120 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 14 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.213006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.183808 restraints weight = 40168.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.186637 restraints weight = 19075.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.188101 restraints weight = 13221.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.188464 restraints weight = 9278.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188843 restraints weight = 9207.890| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8068 Z= 0.130 Angle : 0.494 8.872 11174 Z= 0.259 Chirality : 0.037 0.172 1299 Planarity : 0.004 0.037 1217 Dihedral : 18.894 121.917 1709 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.49 % Allowed : 18.18 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.29), residues: 807 helix: 2.29 (0.28), residues: 348 sheet: -0.32 (0.54), residues: 86 loop : -0.21 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.009 0.001 TYR A1245 PHE 0.014 0.001 PHE A1154 TRP 0.008 0.001 TRP A 555 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8060) covalent geometry : angle 0.49108 / 0.26 (11169) SS BOND : bond 0.00613 / 0.41 ( 1) SS BOND : angle 1.06069 / 0.64 ( 2) hydrogen bonds : bond 0.04623 / 3.09 ( 312) hydrogen bonds : angle 4.53421 / 3.50 ( 885) metal coordination : bond 0.00916 / 0.47 ( 7) metal coordination : angle 3.37480 / 2.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 263 ILE cc_start: 0.8129 (pt) cc_final: 0.7694 (tt) REVERT: A 1141 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.4054 (m-30) outliers start: 11 outliers final: 6 residues processed: 125 average time/residue: 0.1853 time to fit residues: 31.4730 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.214638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.185117 restraints weight = 40474.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.187885 restraints weight = 18919.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.189405 restraints weight = 12750.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.190421 restraints weight = 9023.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.190515 restraints weight = 9184.117| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8068 Z= 0.177 Angle : 0.535 8.304 11174 Z= 0.281 Chirality : 0.038 0.184 1299 Planarity : 0.005 0.050 1217 Dihedral : 18.894 122.598 1709 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.04 % Allowed : 18.18 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.29), residues: 807 helix: 1.92 (0.27), residues: 354 sheet: -0.13 (0.57), residues: 81 loop : -0.36 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.014 0.002 TYR A 562 PHE 0.015 0.002 PHE A 462 TRP 0.008 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 8060) covalent geometry : angle 0.53080 / 0.28 (11169) SS BOND : bond 0.00819 / 0.55 ( 1) SS BOND : angle 1.56183 / 0.88 ( 2) hydrogen bonds : bond 0.04663 / 3.12 ( 312) hydrogen bonds : angle 4.53538 / 3.47 ( 885) metal coordination : bond 0.00997 / 0.51 ( 7) metal coordination : angle 3.93296 / 2.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 356 ASP cc_start: 0.7402 (m-30) cc_final: 0.7195 (m-30) REVERT: A 1141 ASP cc_start: 0.5803 (OUTLIER) cc_final: 0.4063 (m-30) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.1649 time to fit residues: 29.1813 Evaluate side-chains 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.214230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.185698 restraints weight = 40311.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.187647 restraints weight = 18773.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.189223 restraints weight = 13299.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.189723 restraints weight = 9040.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.189910 restraints weight = 8847.040| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8068 Z= 0.141 Angle : 0.508 8.551 11174 Z= 0.267 Chirality : 0.038 0.184 1299 Planarity : 0.004 0.041 1217 Dihedral : 18.878 122.888 1709 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.17 % Allowed : 18.86 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.29), residues: 807 helix: 1.95 (0.28), residues: 354 sheet: -0.20 (0.57), residues: 81 loop : -0.38 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.009 0.002 TYR A1245 PHE 0.015 0.001 PHE A 462 TRP 0.010 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8060) covalent geometry : angle 0.50444 / 0.27 (11169) SS BOND : bond 0.00700 / 0.47 ( 1) SS BOND : angle 1.22522 / 0.73 ( 2) hydrogen bonds : bond 0.04459 / 2.96 ( 312) hydrogen bonds : angle 4.45727 / 3.42 ( 885) metal coordination : bond 0.01001 / 0.50 ( 7) metal coordination : angle 3.79047 / 2.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6817 (tm-30) REVERT: A 263 ILE cc_start: 0.8127 (pt) cc_final: 0.7679 (tt) REVERT: A 384 ASP cc_start: 0.7590 (t0) cc_final: 0.7375 (t0) REVERT: A 1141 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.4077 (m-30) outliers start: 16 outliers final: 13 residues processed: 126 average time/residue: 0.1671 time to fit residues: 29.1230 Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.201479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.171896 restraints weight = 40503.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.174727 restraints weight = 18471.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.176134 restraints weight = 12527.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.177009 restraints weight = 8757.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.177098 restraints weight = 8897.801| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8068 Z= 0.163 Angle : 0.524 8.918 11174 Z= 0.275 Chirality : 0.038 0.187 1299 Planarity : 0.004 0.046 1217 Dihedral : 18.889 123.193 1709 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.58 % Allowed : 18.18 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 807 helix: 1.87 (0.28), residues: 354 sheet: -0.28 (0.57), residues: 81 loop : -0.46 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.012 0.002 TYR A 339 PHE 0.016 0.001 PHE A 462 TRP 0.009 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8060) covalent geometry : angle 0.52036 / 0.27 (11169) SS BOND : bond 0.00776 / 0.52 ( 1) SS BOND : angle 1.45954 / 0.85 ( 2) hydrogen bonds : bond 0.04556 / 3.04 ( 312) hydrogen bonds : angle 4.45618 / 3.40 ( 885) metal coordination : bond 0.01037 / 0.53 ( 7) metal coordination : angle 3.85980 / 2.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 263 ILE cc_start: 0.8181 (pt) cc_final: 0.7762 (tt) REVERT: A 365 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7392 (tp40) REVERT: A 384 ASP cc_start: 0.7605 (t0) cc_final: 0.7385 (t0) REVERT: A 1141 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.4087 (m-30) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.1625 time to fit residues: 28.7312 Evaluate side-chains 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.211539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.181746 restraints weight = 39664.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.184895 restraints weight = 18163.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.186454 restraints weight = 12141.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.186656 restraints weight = 8522.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187078 restraints weight = 8493.016| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8068 Z= 0.149 Angle : 0.517 8.313 11174 Z= 0.271 Chirality : 0.038 0.188 1299 Planarity : 0.004 0.045 1217 Dihedral : 18.883 123.409 1709 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.44 % Allowed : 18.32 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 807 helix: 1.88 (0.28), residues: 353 sheet: -0.32 (0.57), residues: 81 loop : -0.50 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.010 0.002 TYR A1245 PHE 0.015 0.001 PHE A 462 TRP 0.010 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8060) covalent geometry : angle 0.51293 / 0.27 (11169) SS BOND : bond 0.00709 / 0.47 ( 1) SS BOND : angle 1.32879 / 0.79 ( 2) hydrogen bonds : bond 0.04522 / 3.01 ( 312) hydrogen bonds : angle 4.41253 / 3.37 ( 885) metal coordination : bond 0.01029 / 0.52 ( 7) metal coordination : angle 3.84333 / 2.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6837 (tm-30) REVERT: A 263 ILE cc_start: 0.8174 (pt) cc_final: 0.7753 (tt) REVERT: A 365 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7379 (tp40) REVERT: A 1141 ASP cc_start: 0.5801 (OUTLIER) cc_final: 0.4107 (m-30) REVERT: A 1298 ASN cc_start: 0.6621 (m-40) cc_final: 0.6403 (m110) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.1679 time to fit residues: 29.7343 Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.1980 chunk 38 optimal weight: 0.0670 chunk 76 optimal weight: 0.0870 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.202279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.172820 restraints weight = 40590.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.175682 restraints weight = 18760.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.177097 restraints weight = 12695.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.178119 restraints weight = 8788.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.178130 restraints weight = 8974.693| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8068 Z= 0.119 Angle : 0.507 9.034 11174 Z= 0.263 Chirality : 0.037 0.180 1299 Planarity : 0.004 0.045 1217 Dihedral : 18.862 123.159 1709 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.90 % Allowed : 18.59 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 807 helix: 2.00 (0.28), residues: 353 sheet: -0.31 (0.57), residues: 81 loop : -0.45 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.012 0.001 TYR A 948 PHE 0.013 0.001 PHE A 462 TRP 0.010 0.001 TRP A 555 HIS 0.003 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8060) covalent geometry : angle 0.50301 / 0.26 (11169) SS BOND : bond 0.00598 / 0.40 ( 1) SS BOND : angle 1.14769 / 0.71 ( 2) hydrogen bonds : bond 0.04277 / 2.82 ( 312) hydrogen bonds : angle 4.30996 / 3.30 ( 885) metal coordination : bond 0.01096 / 0.54 ( 7) metal coordination : angle 3.61950 / 2.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6824 (tm-30) REVERT: A 263 ILE cc_start: 0.8169 (pt) cc_final: 0.7747 (tt) REVERT: A 561 PHE cc_start: 0.6731 (t80) cc_final: 0.6363 (t80) REVERT: A 1141 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.4825 (m-30) REVERT: A 1298 ASN cc_start: 0.6578 (m-40) cc_final: 0.6255 (m110) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.1717 time to fit residues: 30.0824 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 ASN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.200640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.171151 restraints weight = 40146.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.173995 restraints weight = 18274.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.175375 restraints weight = 12428.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.176350 restraints weight = 8700.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.176388 restraints weight = 8822.300| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8068 Z= 0.161 Angle : 0.534 9.131 11174 Z= 0.280 Chirality : 0.038 0.189 1299 Planarity : 0.004 0.047 1217 Dihedral : 18.892 123.258 1709 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.17 % Allowed : 18.18 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.29), residues: 807 helix: 1.84 (0.28), residues: 353 sheet: -0.37 (0.57), residues: 81 loop : -0.54 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1294 TYR 0.014 0.002 TYR A 948 PHE 0.018 0.002 PHE A 955 TRP 0.009 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8060) covalent geometry : angle 0.52985 / 0.28 (11169) SS BOND : bond 0.00758 / 0.51 ( 1) SS BOND : angle 1.48371 / 0.88 ( 2) hydrogen bonds : bond 0.04510 / 2.99 ( 312) hydrogen bonds : angle 4.37758 / 3.33 ( 885) metal coordination : bond 0.00798 / 0.43 ( 7) metal coordination : angle 3.92957 / 2.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 263 ILE cc_start: 0.8160 (pt) cc_final: 0.7738 (tt) REVERT: A 365 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7440 (tp40) REVERT: A 1141 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.4769 (m-30) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.1662 time to fit residues: 28.2040 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.3980 chunk 47 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.202442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.173047 restraints weight = 40577.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.176124 restraints weight = 18375.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.177503 restraints weight = 12240.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.177772 restraints weight = 8484.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.178085 restraints weight = 8637.980| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8068 Z= 0.109 Angle : 0.505 9.202 11174 Z= 0.261 Chirality : 0.038 0.174 1299 Planarity : 0.004 0.043 1217 Dihedral : 18.849 122.814 1709 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.63 % Allowed : 18.32 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.29), residues: 807 helix: 2.02 (0.28), residues: 353 sheet: -0.32 (0.58), residues: 81 loop : -0.42 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.013 0.001 TYR A 948 PHE 0.012 0.001 PHE A 955 TRP 0.012 0.001 TRP A 555 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8060) covalent geometry : angle 0.50126 / 0.26 (11169) SS BOND : bond 0.00508 / 0.34 ( 1) SS BOND : angle 1.03302 / 0.68 ( 2) hydrogen bonds : bond 0.04122 / 2.71 ( 312) hydrogen bonds : angle 4.24430 / 3.24 ( 885) metal coordination : bond 0.01136 / 0.61 ( 7) metal coordination : angle 3.54609 / 2.50 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6806 (tm-30) REVERT: A 263 ILE cc_start: 0.8129 (pt) cc_final: 0.7708 (tt) REVERT: A 561 PHE cc_start: 0.6761 (t80) cc_final: 0.6413 (t80) REVERT: A 1141 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.3943 (m-30) REVERT: A 1298 ASN cc_start: 0.6415 (m-40) cc_final: 0.6212 (m110) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.1659 time to fit residues: 27.4621 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.202328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.172979 restraints weight = 40221.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.176166 restraints weight = 18099.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.177469 restraints weight = 12139.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.177685 restraints weight = 8414.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.178003 restraints weight = 8544.063| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.265 8068 Z= 0.241 Angle : 0.873 59.200 11174 Z= 0.548 Chirality : 0.052 1.290 1299 Planarity : 0.004 0.051 1217 Dihedral : 18.851 122.827 1709 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.63 % Allowed : 18.32 % Favored : 80.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.29), residues: 807 helix: 2.02 (0.28), residues: 353 sheet: -0.33 (0.58), residues: 81 loop : -0.40 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.010 0.001 TYR A 948 PHE 0.012 0.001 PHE A 462 TRP 0.012 0.001 TRP A 555 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.24 ( 8060) covalent geometry : angle 0.87125 / 0.55 (11169) SS BOND : bond 0.00541 / 0.36 ( 1) SS BOND : angle 1.04039 / 0.69 ( 2) hydrogen bonds : bond 0.04126 / 2.71 ( 312) hydrogen bonds : angle 4.24389 / 3.24 ( 885) metal coordination : bond 0.01089 / 0.58 ( 7) metal coordination : angle 3.54817 / 2.50 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.40 seconds wall clock time: 43 minutes 55.09 seconds (2635.09 seconds total)