Starting phenix.real_space_refine on Fri Jun 13 13:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opt_17087/06_2025/8opt_17087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opt_17087/06_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_17087/06_2025/8opt_17087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opt_17087/06_2025/8opt_17087.map" model { file = "/net/cci-nas-00/data/ceres_data/8opt_17087/06_2025/8opt_17087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opt_17087/06_2025/8opt_17087.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: 8.20, per 1000 atoms: 0.55 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: 4.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 6.60 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: 5.68 Time building geometry restraints manager: 5.12 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: 2.860 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: 0.230 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 46.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- 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 : 7.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (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 TRP 0.005 0.001 TRP A 555 HIS 0.002 0.001 HIS A 422 PHE 0.007 0.001 PHE A 955 TYR 0.010 0.001 TYR A1245 ARG 0.005 0.000 ARG A 970 Details of bonding type rmsd hydrogen bonds : bond 0.12020 ( 312) hydrogen bonds : angle 5.09320 ( 885) metal coordination : bond 0.00541 ( 7) metal coordination : angle 1.87773 ( 3) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.86277 ( 2) covalent geometry : bond 0.00218 ( 8060) covalent geometry : angle 0.47782 (11169) *********************** 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 : 1.156 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: 0.4363 time to fit residues: 63.7447 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 : 1.084 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4662 r_free = 0.4662 target = 0.202893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.173126 restraints weight = 40318.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.175946 restraints weight = 18797.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.177480 restraints weight = 12450.351| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8068 Z= 0.208 Angle : 0.570 6.844 11174 Z= 0.300 Chirality : 0.038 0.162 1299 Planarity : 0.005 0.043 1217 Dihedral : 18.966 122.981 1711 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.63 % Allowed : 18.45 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 807 helix: 2.27 (0.27), residues: 341 sheet: -0.31 (0.54), residues: 86 loop : -0.25 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 PHE 0.019 0.002 PHE A1154 TYR 0.018 0.002 TYR A 562 ARG 0.005 0.001 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 312) hydrogen bonds : angle 4.68185 ( 885) metal coordination : bond 0.01033 ( 7) metal coordination : angle 4.35338 ( 3) SS BOND : bond 0.00883 ( 1) SS BOND : angle 1.57215 ( 2) covalent geometry : bond 0.00468 ( 8060) covalent geometry : angle 0.56572 (11169) *********************** 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 133 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.079 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 311 GLU cc_start: 0.6818 (mp0) cc_final: 0.6565 (mp0) REVERT: A 1141 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.4245 (m-30) outliers start: 12 outliers final: 7 residues processed: 128 average time/residue: 0.4695 time to fit residues: 80.4207 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 9 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.215295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.185920 restraints weight = 40319.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.188547 restraints weight = 19942.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.189944 restraints weight = 13651.956| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.1071 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= 0.127 Angle : 0.503 8.849 11174 Z= 0.259 Chirality : 0.036 0.128 1299 Planarity : 0.004 0.039 1217 Dihedral : 18.882 122.944 1709 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.22 % Allowed : 19.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 807 helix: 2.22 (0.28), residues: 348 sheet: -0.37 (0.55), residues: 86 loop : -0.18 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.005 0.001 HIS A 260 PHE 0.014 0.001 PHE A 462 TYR 0.010 0.001 TYR A1245 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 312) hydrogen bonds : angle 4.44825 ( 885) metal coordination : bond 0.01060 ( 7) metal coordination : angle 3.46582 ( 3) SS BOND : bond 0.00637 ( 1) SS BOND : angle 1.17491 ( 2) covalent geometry : bond 0.00290 ( 8060) covalent geometry : angle 0.50007 (11169) *********************** 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 126 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.964 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 263 ILE cc_start: 0.8149 (pt) cc_final: 0.7716 (tt) outliers start: 9 outliers final: 7 residues processed: 124 average time/residue: 0.4450 time to fit residues: 73.7352 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 : 0.965 ------------------------------------------------------------------------------- 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 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 1292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.211358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.182219 restraints weight = 39813.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.185114 restraints weight = 18612.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.186369 restraints weight = 12814.682| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.1453 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= 0.162 Angle : 0.532 7.025 11174 Z= 0.277 Chirality : 0.037 0.140 1299 Planarity : 0.004 0.044 1217 Dihedral : 18.897 123.505 1709 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.44 % Allowed : 19.00 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 807 helix: 1.90 (0.27), residues: 354 sheet: -0.20 (0.57), residues: 81 loop : -0.32 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.015 0.001 PHE A 462 TYR 0.013 0.002 TYR A 562 ARG 0.003 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 312) hydrogen bonds : angle 4.46313 ( 885) metal coordination : bond 0.01033 ( 7) metal coordination : angle 3.95804 ( 3) SS BOND : bond 0.00789 ( 1) SS BOND : angle 1.42259 ( 2) covalent geometry : bond 0.00369 ( 8060) covalent geometry : angle 0.52813 (11169) *********************** 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 135 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.961 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: 0.8163 (pt) cc_final: 0.7744 (tt) REVERT: A 356 ASP cc_start: 0.7381 (m-30) cc_final: 0.7150 (m-30) REVERT: A 384 ASP cc_start: 0.7575 (t0) cc_final: 0.7361 (t0) REVERT: A 1141 ASP cc_start: 0.5866 (OUTLIER) cc_final: 0.4473 (m-30) REVERT: A 1310 VAL cc_start: 0.8157 (p) cc_final: 0.7948 (t) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.4209 time to fit residues: 74.4161 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4696 r_free = 0.4696 target = 0.214460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.185040 restraints weight = 40213.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188239 restraints weight = 18532.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.189653 restraints weight = 12241.182| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.1567 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= 0.132 Angle : 0.512 7.845 11174 Z= 0.264 Chirality : 0.036 0.130 1299 Planarity : 0.004 0.044 1217 Dihedral : 18.869 123.727 1709 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 19.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 807 helix: 1.98 (0.28), residues: 353 sheet: -0.23 (0.57), residues: 81 loop : -0.34 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.003 0.001 HIS A 973 PHE 0.014 0.001 PHE A 462 TYR 0.011 0.001 TYR A 948 ARG 0.004 0.000 ARG A 970 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 312) hydrogen bonds : angle 4.37228 ( 885) metal coordination : bond 0.01057 ( 7) metal coordination : angle 3.74388 ( 3) SS BOND : bond 0.00664 ( 1) SS BOND : angle 1.23377 ( 2) covalent geometry : bond 0.00304 ( 8060) covalent geometry : angle 0.50768 (11169) *********************** 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 : 1.207 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 263 ILE cc_start: 0.8180 (pt) cc_final: 0.7760 (tt) REVERT: A 365 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: A 1298 ASN cc_start: 0.6594 (m-40) cc_final: 0.6378 (m110) REVERT: A 1310 VAL cc_start: 0.8111 (p) cc_final: 0.7885 (t) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 0.4328 time to fit residues: 74.8496 Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4645 r_free = 0.4645 target = 0.201761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.172272 restraints weight = 40279.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.175218 restraints weight = 18302.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.176606 restraints weight = 12332.443| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.1740 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= 0.138 Angle : 0.513 7.851 11174 Z= 0.265 Chirality : 0.037 0.132 1299 Planarity : 0.004 0.046 1217 Dihedral : 18.868 123.532 1709 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.17 % Allowed : 19.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 807 helix: 1.95 (0.28), residues: 353 sheet: -0.26 (0.57), residues: 81 loop : -0.34 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.014 0.001 PHE A 462 TYR 0.012 0.002 TYR A 948 ARG 0.003 0.000 ARG A 970 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 312) hydrogen bonds : angle 4.33702 ( 885) metal coordination : bond 0.01014 ( 7) metal coordination : angle 3.70118 ( 3) SS BOND : bond 0.00675 ( 1) SS BOND : angle 1.24968 ( 2) covalent geometry : bond 0.00319 ( 8060) covalent geometry : angle 0.50937 (11169) *********************** 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 132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.014 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 263 ILE cc_start: 0.8188 (pt) cc_final: 0.7756 (tt) REVERT: A 365 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7357 (tp40) REVERT: A 1141 ASP cc_start: 0.5724 (OUTLIER) cc_final: 0.5083 (m-30) REVERT: A 1298 ASN cc_start: 0.6598 (m-40) cc_final: 0.6363 (m110) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.4332 time to fit residues: 75.3393 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 : 0.977 ------------------------------------------------------------------------------- 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 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 1322 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 413 ASN A1193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.212799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.183880 restraints weight = 39998.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.186742 restraints weight = 18689.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.187994 restraints weight = 12712.361| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.1817 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= 0.124 Angle : 0.510 8.241 11174 Z= 0.263 Chirality : 0.037 0.129 1299 Planarity : 0.004 0.045 1217 Dihedral : 18.856 123.280 1709 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 807 helix: 1.99 (0.28), residues: 353 sheet: -0.25 (0.58), residues: 81 loop : -0.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 555 HIS 0.003 0.001 HIS A 973 PHE 0.013 0.001 PHE A 462 TYR 0.012 0.001 TYR A 948 ARG 0.002 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 312) hydrogen bonds : angle 4.29941 ( 885) metal coordination : bond 0.01000 ( 7) metal coordination : angle 3.53330 ( 3) SS BOND : bond 0.00585 ( 1) SS BOND : angle 1.16428 ( 2) covalent geometry : bond 0.00285 ( 8060) covalent geometry : angle 0.50693 (11169) *********************** 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 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.041 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: 0.8159 (pt) cc_final: 0.7728 (tt) REVERT: A 1141 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.5023 (m-30) REVERT: A 1298 ASN cc_start: 0.6568 (m-40) cc_final: 0.6245 (m110) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 0.4674 time to fit residues: 79.0545 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 1322 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.0010 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.202859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.173525 restraints weight = 40228.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.176600 restraints weight = 18382.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.178005 restraints weight = 12256.380| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.1878 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= 0.107 Angle : 0.500 8.230 11174 Z= 0.256 Chirality : 0.036 0.134 1299 Planarity : 0.005 0.103 1217 Dihedral : 18.836 122.506 1709 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.44 % Allowed : 18.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 807 helix: 2.11 (0.28), residues: 353 sheet: -0.24 (0.58), residues: 81 loop : -0.23 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 555 HIS 0.003 0.001 HIS A 422 PHE 0.011 0.001 PHE A 955 TYR 0.011 0.001 TYR A 948 ARG 0.007 0.000 ARG A1294 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 312) hydrogen bonds : angle 4.18687 ( 885) metal coordination : bond 0.00904 ( 7) metal coordination : angle 3.25907 ( 3) SS BOND : bond 0.00553 ( 1) SS BOND : angle 1.05271 ( 2) covalent geometry : bond 0.00247 ( 8060) covalent geometry : angle 0.49671 (11169) *********************** 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: 18 poor density : 112 time to evaluate : 1.090 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 263 ILE cc_start: 0.8172 (pt) cc_final: 0.7754 (tt) REVERT: A 1298 ASN cc_start: 0.6422 (m-40) cc_final: 0.6184 (m110) outliers start: 18 outliers final: 14 residues processed: 125 average time/residue: 0.4734 time to fit residues: 78.7931 Evaluate side-chains 121 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 370 LEU 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 1153 VAL Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1294 ARG 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 65 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.214689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185708 restraints weight = 39994.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188261 restraints weight = 19167.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.190236 restraints weight = 12132.535| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8068 Z= 0.116 Angle : 0.514 8.933 11174 Z= 0.267 Chirality : 0.037 0.144 1299 Planarity : 0.004 0.048 1217 Dihedral : 18.835 122.230 1709 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.04 % Allowed : 19.67 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.30), residues: 807 helix: 2.09 (0.28), residues: 353 sheet: -0.29 (0.57), residues: 81 loop : -0.20 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.003 0.001 HIS A 422 PHE 0.015 0.001 PHE A 955 TYR 0.011 0.001 TYR A1245 ARG 0.002 0.000 ARG A1294 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 312) hydrogen bonds : angle 4.19370 ( 885) metal coordination : bond 0.01290 ( 7) metal coordination : angle 2.86200 ( 3) SS BOND : bond 0.00551 ( 1) SS BOND : angle 1.06635 ( 2) covalent geometry : bond 0.00267 ( 8060) covalent geometry : angle 0.51175 (11169) *********************** 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: 15 poor density : 113 time to evaluate : 0.996 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 263 ILE cc_start: 0.8175 (pt) cc_final: 0.7759 (tt) REVERT: A 284 LEU cc_start: 0.6656 (mt) cc_final: 0.6287 (mp) outliers start: 15 outliers final: 14 residues processed: 124 average time/residue: 0.4575 time to fit residues: 74.8637 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 : 0.982 ------------------------------------------------------------------------------- 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 370 LEU 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 1153 VAL Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1294 ARG 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 60 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A1193 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.199347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.170248 restraints weight = 40344.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.173265 restraints weight = 18445.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.174593 restraints weight = 12402.564| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.2302 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= 0.180 Angle : 0.568 8.503 11174 Z= 0.298 Chirality : 0.038 0.142 1299 Planarity : 0.004 0.047 1217 Dihedral : 18.909 123.330 1709 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.90 % Allowed : 19.81 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.29), residues: 807 helix: 1.63 (0.28), residues: 354 sheet: -0.46 (0.57), residues: 81 loop : -0.39 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 PHE 0.017 0.002 PHE A1154 TYR 0.013 0.002 TYR A 562 ARG 0.004 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 312) hydrogen bonds : angle 4.42822 ( 885) metal coordination : bond 0.01271 ( 7) metal coordination : angle 3.74988 ( 3) SS BOND : bond 0.00783 ( 1) SS BOND : angle 1.55269 ( 2) covalent geometry : bond 0.00414 ( 8060) covalent geometry : angle 0.56474 (11169) ********************** 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 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.023 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: 0.8190 (pt) cc_final: 0.7751 (tt) REVERT: A 1157 MET cc_start: 0.6770 (mmp) cc_final: 0.6570 (mmp) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.4740 time to fit residues: 77.5636 Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 1140 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1294 ARG 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 8 optimal weight: 0.0070 chunk 65 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A1193 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.208000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.181829 restraints weight = 40908.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.184229 restraints weight = 20172.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.185716 restraints weight = 12936.763| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8068 Z= 0.111 Angle : 0.529 9.489 11174 Z= 0.273 Chirality : 0.037 0.138 1299 Planarity : 0.004 0.043 1217 Dihedral : 18.840 123.122 1709 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.49 % Allowed : 20.22 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.30), residues: 807 helix: 1.81 (0.28), residues: 354 sheet: -0.39 (0.58), residues: 81 loop : -0.30 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.003 0.001 HIS A 422 PHE 0.012 0.001 PHE A 462 TYR 0.013 0.001 TYR A 626 ARG 0.002 0.000 ARG A1294 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 312) hydrogen bonds : angle 4.26414 ( 885) metal coordination : bond 0.01331 ( 7) metal coordination : angle 2.84957 ( 3) SS BOND : bond 0.00516 ( 1) SS BOND : angle 1.09199 ( 2) covalent geometry : bond 0.00253 ( 8060) covalent geometry : angle 0.52698 (11169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5608.09 seconds wall clock time: 96 minutes 16.32 seconds (5776.32 seconds total)