Starting phenix.real_space_refine on Sat Aug 23 22:10:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opt_17087/08_2025/8opt_17087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opt_17087/08_2025/8opt_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_2025/8opt_17087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2025/8opt_17087.map" model { file = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2025/8opt_17087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opt_17087/08_2025/8opt_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.32, per 1000 atoms: 0.15 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: 0.93 Conformation dependent library (CDL) restraints added in 303.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.80 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: 3.05 Time building geometry restraints manager: 1.25 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=" 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 bond pdb=" CB GLU A1327 " pdb=" CG GLU A1327 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.76e-01 ... (remaining 15252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 27260 1.78 - 3.57: 326 3.57 - 5.35: 19 5.35 - 7.14: 1 7.14 - 8.92: 1 Bond angle restraints: 27607 Sorted by residual: angle pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " pdb=" CD LYS A 270 " ideal model delta sigma weight residual 111.30 117.96 -6.66 2.30e+00 1.89e-01 8.39e+00 angle pdb=" CA LEU A 214 " pdb=" CB LEU A 214 " pdb=" CG LEU A 214 " ideal model delta sigma weight residual 116.30 125.22 -8.92 3.50e+00 8.16e-02 6.50e+00 angle pdb=" C4' C D 48 " pdb=" C3' C D 48 " pdb=" O3' C D 48 " ideal model delta sigma weight residual 109.40 112.76 -3.36 1.50e+00 4.44e-01 5.02e+00 angle pdb=" C VAL A1206 " pdb=" N ASP A1207 " pdb=" CA ASP A1207 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" CA GLU A 222 " pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " ideal model delta sigma weight residual 114.10 118.09 -3.99 2.00e+00 2.50e-01 3.98e+00 ... (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: 852 0.026 - 0.051: 300 0.051 - 0.077: 69 0.077 - 0.103: 41 0.103 - 0.129: 37 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: 3.830 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: 0.050 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 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= 0.096 Angle : 0.479 8.923 11174 Z= 0.245 Chirality : 0.035 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 aren 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 covalent geometry : bond 0.00218 ( 8060) covalent geometry : angle 0.47782 (11169) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.86277 ( 2) hydrogen bonds : bond 0.12020 ( 312) hydrogen bonds : angle 5.09320 ( 885) metal coordination : bond 0.00541 ( 7) metal coordination : angle 1.87773 ( 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 : 0.336 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: 0.1438 time to fit residues: 20.7759 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 : 0.235 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4666 r_free = 0.4666 target = 0.203208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.173449 restraints weight = 40522.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.176271 restraints weight = 19093.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.177922 restraints weight = 12358.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.178674 restraints weight = 8687.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.178854 restraints weight = 9013.750| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8068 Z= 0.198 Angle : 0.559 6.561 11174 Z= 0.294 Chirality : 0.038 0.156 1299 Planarity : 0.004 0.044 1217 Dihedral : 18.952 122.661 1711 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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 aren not related in a simple way. whole: 1.28 (0.29), residues: 807 helix: 2.34 (0.28), residues: 341 sheet: -0.30 (0.54), residues: 86 loop : -0.23 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 583 TYR 0.017 0.002 TYR A 562 PHE 0.018 0.002 PHE A1154 TRP 0.008 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8060) covalent geometry : angle 0.55464 (11169) SS BOND : bond 0.00838 ( 1) SS BOND : angle 1.48029 ( 2) hydrogen bonds : bond 0.04634 ( 312) hydrogen bonds : angle 4.65047 ( 885) metal coordination : bond 0.01012 ( 7) metal coordination : angle 4.15580 ( 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 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.247 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: A 311 GLU cc_start: 0.6782 (mp0) cc_final: 0.6538 (mp0) REVERT: A 1141 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.4152 (m-30) outliers start: 12 outliers final: 7 residues processed: 125 average time/residue: 0.1705 time to fit residues: 28.5824 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 420 THR 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 1220 LEU 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: 0.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 79 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4707 r_free = 0.4707 target = 0.213240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.184276 restraints weight = 40229.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186952 restraints weight = 19541.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.188460 restraints weight = 13640.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.188963 restraints weight = 9374.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.189319 restraints weight = 9359.685| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.1083 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= 0.142 Angle : 0.511 8.834 11174 Z= 0.264 Chirality : 0.037 0.132 1299 Planarity : 0.004 0.040 1217 Dihedral : 18.894 123.107 1709 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.49 % Allowed : 18.45 % 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 aren not related in a simple way. whole: 1.18 (0.29), residues: 807 helix: 2.13 (0.28), residues: 348 sheet: -0.35 (0.55), residues: 86 loop : -0.20 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 576 TYR 0.011 0.002 TYR A1245 PHE 0.015 0.001 PHE A 462 TRP 0.008 0.001 TRP A 555 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8060) covalent geometry : angle 0.50724 (11169) SS BOND : bond 0.00677 ( 1) SS BOND : angle 1.27849 ( 2) hydrogen bonds : bond 0.04285 ( 312) hydrogen bonds : angle 4.48478 ( 885) metal coordination : bond 0.01018 ( 7) metal coordination : angle 3.63745 ( 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 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.294 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 263 ILE cc_start: 0.8140 (pt) cc_final: 0.7704 (tt) REVERT: A 1141 ASP cc_start: 0.5701 (OUTLIER) cc_final: 0.4934 (m-30) REVERT: A 1310 VAL cc_start: 0.8123 (p) cc_final: 0.7913 (t) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.1790 time to fit residues: 30.4547 Evaluate side-chains 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.213966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.185142 restraints weight = 40303.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.188019 restraints weight = 19226.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.189285 restraints weight = 13125.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.189541 restraints weight = 9062.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.189895 restraints weight = 9010.339| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8068 Z= 0.115 Angle : 0.494 7.663 11174 Z= 0.255 Chirality : 0.036 0.128 1299 Planarity : 0.004 0.041 1217 Dihedral : 18.844 122.465 1709 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.76 % Allowed : 18.45 % 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 aren not related in a simple way. whole: 1.27 (0.29), residues: 807 helix: 2.27 (0.28), residues: 348 sheet: -0.37 (0.55), residues: 86 loop : -0.20 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.011 0.001 TYR A1245 PHE 0.012 0.001 PHE A 462 TRP 0.008 0.001 TRP A 555 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8060) covalent geometry : angle 0.49148 (11169) SS BOND : bond 0.00597 ( 1) SS BOND : angle 1.09693 ( 2) hydrogen bonds : bond 0.03822 ( 312) hydrogen bonds : angle 4.31906 ( 885) metal coordination : bond 0.00954 ( 7) metal coordination : angle 3.26214 ( 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 133 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.345 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 263 ILE cc_start: 0.8146 (pt) cc_final: 0.7738 (tt) REVERT: A 356 ASP cc_start: 0.7362 (m-30) cc_final: 0.7144 (m-30) REVERT: A 384 ASP cc_start: 0.7561 (t0) cc_final: 0.7339 (t0) REVERT: A 1141 ASP cc_start: 0.5637 (OUTLIER) cc_final: 0.4795 (m-30) REVERT: A 1310 VAL cc_start: 0.8081 (p) cc_final: 0.7871 (t) outliers start: 13 outliers final: 8 residues processed: 130 average time/residue: 0.1818 time to fit residues: 31.6384 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4699 r_free = 0.4699 target = 0.214664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.185224 restraints weight = 40213.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.188212 restraints weight = 18794.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.189604 restraints weight = 12495.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.190625 restraints weight = 8742.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.190706 restraints weight = 8863.905| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8068 Z= 0.137 Angle : 0.513 7.824 11174 Z= 0.264 Chirality : 0.037 0.133 1299 Planarity : 0.004 0.044 1217 Dihedral : 18.868 123.102 1709 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.44 % Allowed : 18.45 % Favored : 79.10 % 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 aren not related in a simple way. whole: 1.10 (0.29), residues: 807 helix: 2.02 (0.28), residues: 353 sheet: -0.22 (0.56), residues: 81 loop : -0.27 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 970 TYR 0.011 0.002 TYR A 948 PHE 0.013 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 covalent geometry : bond 0.00314 ( 8060) covalent geometry : angle 0.50917 (11169) SS BOND : bond 0.00680 ( 1) SS BOND : angle 1.27519 ( 2) hydrogen bonds : bond 0.04052 ( 312) hydrogen bonds : angle 4.32332 ( 885) metal coordination : bond 0.00822 ( 7) metal coordination : angle 3.78597 ( 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 132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.318 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 263 ILE cc_start: 0.8181 (pt) cc_final: 0.7770 (tt) REVERT: A 356 ASP cc_start: 0.7414 (m-30) cc_final: 0.7135 (m-30) REVERT: A 1141 ASP cc_start: 0.5745 (OUTLIER) cc_final: 0.4851 (m-30) REVERT: A 1310 VAL cc_start: 0.8103 (p) cc_final: 0.7888 (t) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.1675 time to fit residues: 29.1506 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 : 0.231 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 86 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4645 r_free = 0.4645 target = 0.201762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.172311 restraints weight = 40346.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.175604 restraints weight = 18695.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.176958 restraints weight = 11977.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.177150 restraints weight = 8300.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.177326 restraints weight = 8417.843| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.1728 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 : 0.513 7.650 11174 Z= 0.265 Chirality : 0.037 0.132 1299 Planarity : 0.004 0.045 1217 Dihedral : 18.865 123.508 1709 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.71 % Allowed : 18.18 % Favored : 79.10 % 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 aren not related in a simple way. whole: 1.06 (0.29), residues: 807 helix: 2.02 (0.28), residues: 353 sheet: -0.25 (0.57), residues: 81 loop : -0.33 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.011 0.002 TYR A1245 PHE 0.014 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 covalent geometry : bond 0.00327 ( 8060) covalent geometry : angle 0.50988 (11169) SS BOND : bond 0.00681 ( 1) SS BOND : angle 1.27865 ( 2) hydrogen bonds : bond 0.04066 ( 312) hydrogen bonds : angle 4.30162 ( 885) metal coordination : bond 0.00940 ( 7) metal coordination : angle 3.60314 ( 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 138 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.259 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: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8188 (pt) cc_final: 0.7770 (tt) REVERT: A 356 ASP cc_start: 0.7403 (m-30) cc_final: 0.7137 (m-30) REVERT: A 365 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: A 1141 ASP cc_start: 0.5739 (OUTLIER) cc_final: 0.4873 (m-30) REVERT: A 1298 ASN cc_start: 0.6590 (m-40) cc_final: 0.6372 (m110) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.1602 time to fit residues: 28.9760 Evaluate side-chains 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 0.0870 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 350 ASN A1193 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.201485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.172085 restraints weight = 40022.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.175244 restraints weight = 18179.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.176569 restraints weight = 12103.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.176801 restraints weight = 8453.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.177005 restraints weight = 8460.774| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8068 Z= 0.136 Angle : 0.516 8.273 11174 Z= 0.265 Chirality : 0.037 0.130 1299 Planarity : 0.004 0.045 1217 Dihedral : 18.865 123.444 1709 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.31 % Allowed : 18.72 % 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 aren not related in a simple way. whole: 1.04 (0.29), residues: 807 helix: 2.02 (0.28), residues: 353 sheet: -0.31 (0.57), residues: 81 loop : -0.34 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.012 0.001 TYR A 948 PHE 0.014 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 covalent geometry : bond 0.00316 ( 8060) covalent geometry : angle 0.51218 (11169) SS BOND : bond 0.00647 ( 1) SS BOND : angle 1.26438 ( 2) hydrogen bonds : bond 0.04050 ( 312) hydrogen bonds : angle 4.26813 ( 885) metal coordination : bond 0.00913 ( 7) metal coordination : angle 3.62896 ( 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 132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8184 (pt) cc_final: 0.7763 (tt) REVERT: A 1141 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.4829 (m-30) REVERT: A 1298 ASN cc_start: 0.6592 (m-40) cc_final: 0.6372 (m110) outliers start: 17 outliers final: 16 residues processed: 129 average time/residue: 0.1554 time to fit residues: 26.9828 Evaluate side-chains 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1258 ILE 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: 0.7980 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 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 = 0.4677 r_free = 0.4677 target = 0.211999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.183346 restraints weight = 39769.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.186747 restraints weight = 18472.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187947 restraints weight = 11984.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.188160 restraints weight = 8287.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.188352 restraints weight = 8270.466| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8068 Z= 0.159 Angle : 0.532 8.220 11174 Z= 0.275 Chirality : 0.037 0.135 1299 Planarity : 0.004 0.047 1217 Dihedral : 18.882 123.630 1709 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.31 % Allowed : 18.86 % Favored : 78.83 % 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 aren not related in a simple way. whole: 0.93 (0.29), residues: 807 helix: 1.90 (0.28), residues: 354 sheet: -0.36 (0.57), residues: 81 loop : -0.38 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.012 0.002 TYR A 948 PHE 0.015 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 covalent geometry : bond 0.00366 ( 8060) covalent geometry : angle 0.52799 (11169) SS BOND : bond 0.00736 ( 1) SS BOND : angle 1.37002 ( 2) hydrogen bonds : bond 0.04239 ( 312) hydrogen bonds : angle 4.33858 ( 885) metal coordination : bond 0.00928 ( 7) metal coordination : angle 3.81045 ( 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 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.266 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: symmetry clash revert: symmetry clash REVERT: A 365 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7325 (tp40) REVERT: A 1141 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.4892 (m-30) REVERT: A 1298 ASN cc_start: 0.6580 (m-40) cc_final: 0.6265 (m110) outliers start: 17 outliers final: 13 residues processed: 126 average time/residue: 0.1600 time to fit residues: 27.2877 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 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 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 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 1322 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 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 = 0.4677 r_free = 0.4677 target = 0.212718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.183605 restraints weight = 39661.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.186662 restraints weight = 18561.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.188052 restraints weight = 12121.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.188996 restraints weight = 8510.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.189098 restraints weight = 8669.403| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8068 Z= 0.143 Angle : 0.530 8.715 11174 Z= 0.274 Chirality : 0.037 0.130 1299 Planarity : 0.004 0.046 1217 Dihedral : 18.875 123.463 1709 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.44 % Allowed : 18.59 % 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 aren not related in a simple way. whole: 0.93 (0.29), residues: 807 helix: 1.89 (0.28), residues: 353 sheet: -0.35 (0.58), residues: 81 loop : -0.36 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.012 0.002 TYR A 948 PHE 0.014 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 covalent geometry : bond 0.00331 ( 8060) covalent geometry : angle 0.52574 (11169) SS BOND : bond 0.00670 ( 1) SS BOND : angle 1.29978 ( 2) hydrogen bonds : bond 0.04173 ( 312) hydrogen bonds : angle 4.28969 ( 885) metal coordination : bond 0.00922 ( 7) metal coordination : angle 3.83489 ( 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 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 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: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8051 (pt) cc_final: 0.7623 (tt) REVERT: A 365 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7361 (tp40) REVERT: A 1141 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.4881 (m-30) REVERT: A 1298 ASN cc_start: 0.6474 (m-40) cc_final: 0.6272 (m110) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.1566 time to fit residues: 26.5657 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 329 HIS Chi-restraints excluded: chain A residue 350 ASN 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 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 1322 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.0050 chunk 47 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 0.0770 chunk 64 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 46 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.1330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.214006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.185380 restraints weight = 40154.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.188544 restraints weight = 18657.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.189810 restraints weight = 12259.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.190312 restraints weight = 8553.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.190521 restraints weight = 8522.414| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.2065 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= 0.099 Angle : 0.502 9.134 11174 Z= 0.257 Chirality : 0.037 0.150 1299 Planarity : 0.004 0.043 1217 Dihedral : 18.806 122.093 1709 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.36 % Allowed : 19.95 % Favored : 78.70 % 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 aren not related in a simple way. whole: 1.25 (0.30), residues: 807 helix: 2.29 (0.28), residues: 347 sheet: -0.47 (0.57), residues: 86 loop : -0.21 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 441 TYR 0.009 0.001 TYR A1245 PHE 0.013 0.001 PHE A 382 TRP 0.013 0.001 TRP A 555 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8060) covalent geometry : angle 0.49938 (11169) SS BOND : bond 0.00486 ( 1) SS BOND : angle 0.98495 ( 2) hydrogen bonds : bond 0.03562 ( 312) hydrogen bonds : angle 4.09350 ( 885) metal coordination : bond 0.00811 ( 7) metal coordination : angle 2.86088 ( 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 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.238 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: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7989 (pt) cc_final: 0.7593 (tt) REVERT: A 284 LEU cc_start: 0.6643 (mt) cc_final: 0.6267 (mp) REVERT: A 1298 ASN cc_start: 0.6432 (m-40) cc_final: 0.6191 (m110) outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 0.1801 time to fit residues: 29.5096 Evaluate side-chains 121 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 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 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: 0.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.212781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.184020 restraints weight = 39692.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.186531 restraints weight = 18681.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.188078 restraints weight = 12239.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.189032 restraints weight = 8672.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189061 restraints weight = 8656.548| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8068 Z= 0.144 Angle : 0.538 8.835 11174 Z= 0.277 Chirality : 0.037 0.138 1299 Planarity : 0.004 0.048 1217 Dihedral : 18.859 121.966 1709 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.09 % Allowed : 20.49 % Favored : 78.43 % 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 aren not related in a simple way. whole: 1.08 (0.29), residues: 807 helix: 1.99 (0.28), residues: 354 sheet: -0.25 (0.59), residues: 81 loop : -0.27 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 560 TYR 0.011 0.001 TYR A1245 PHE 0.020 0.002 PHE A1244 TRP 0.009 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8060) covalent geometry : angle 0.53438 (11169) SS BOND : bond 0.00644 ( 1) SS BOND : angle 1.29466 ( 2) hydrogen bonds : bond 0.04075 ( 312) hydrogen bonds : angle 4.21262 ( 885) metal coordination : bond 0.00883 ( 7) metal coordination : angle 3.62131 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.93 seconds wall clock time: 40 minutes 39.92 seconds (2439.92 seconds total)