Starting phenix.real_space_refine on Thu Oct 22 23:41:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzr_66405/10_2026/9wzr_66405.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzr_66405/10_2026/9wzr_66405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wzr_66405/10_2026/9wzr_66405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzr_66405/10_2026/9wzr_66405.map" model { file = "/net/cci-nas-00/data/ceres_data/9wzr_66405/10_2026/9wzr_66405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzr_66405/10_2026/9wzr_66405.cif" } resolution = 3.21 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= -0.000 sd= 0.033 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: 6 Type Number sf(0) Gaussians P 103 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 3837 2.51 5 N 1283 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6757 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4606 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 19, 'TRANS': 561} Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1000 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 20, 'rna3p_pyr': 20} Link IDs: {'rna2p': 7, 'rna3p': 39} Chain: "C" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 593 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.43, per 1000 atoms: 0.21 Number of scatterers: 6757 At special positions: 0 Unit cell: (94.72, 94.72, 109.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 103 15.00 Mg 1 11.99 O 1515 8.00 N 1283 7.00 C 3837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 260.3 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1088 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 52.7% alpha, 20.8% beta 26 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 31 through 64 removed outlier: 4.446A pdb=" N GLU A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 64 " --> pdb=" O ARG A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 98 Processing helix chain 'A' and resid 105 through 137 Proline residue: A 121 - end of helix removed outlier: 3.626A pdb=" N ALA A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 158 removed outlier: 3.520A pdb=" N LEU A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 184 removed outlier: 3.705A pdb=" N ARG A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 355 through 387 removed outlier: 3.781A pdb=" N VAL A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 421 through 433 removed outlier: 3.574A pdb=" N LYS A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 488 Processing helix chain 'A' and resid 497 through 503 removed outlier: 3.670A pdb=" N LEU A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.613A pdb=" N LEU A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.027A pdb=" N ALA A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 207 removed outlier: 13.314A pdb=" N GLY A 196 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N ARG A 280 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N LEU A 198 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N ARG A 278 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ASN A 200 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N ASN A 276 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N ILE A 202 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 11.195A pdb=" N ALA A 274 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N GLY A 204 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N GLU A 272 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 270 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN A 311 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 272 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR A 299 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N VAL A 284 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N ILE A 297 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 12.282A pdb=" N SER A 286 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 14.090A pdb=" N ARG A 295 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR A 304 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 24 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 23 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG A 252 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 225 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 234 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU A 223 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR A 236 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 221 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 354 removed outlier: 6.564A pdb=" N GLU A 350 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A 341 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 352 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 337 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS A 331 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 339 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 494 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 328 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 491 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N HIS A 548 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 493 " --> pdb=" O HIS A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 563 through 564 280 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 948 1.32 - 1.44: 2419 1.44 - 1.56: 3489 1.56 - 1.69: 202 1.69 - 1.81: 29 Bond restraints: 7087 Sorted by residual: bond pdb=" CA TYR A 528 " pdb=" C TYR A 528 " ideal model delta sigma weight residual 1.524 1.460 0.063 1.29e-02 6.01e+03 2.40e+01 bond pdb=" O3' DC D -5 " pdb=" P DT D -4 " ideal model delta sigma weight residual 1.607 1.554 0.053 1.20e-02 6.94e+03 1.92e+01 bond pdb=" N ASP A 186 " pdb=" CA ASP A 186 " ideal model delta sigma weight residual 1.458 1.408 0.050 1.19e-02 7.06e+03 1.75e+01 bond pdb=" C TYR A 528 " pdb=" O TYR A 528 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" C3' DC D 9 " pdb=" C2' DC D 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 7082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 9270 1.30 - 2.61: 591 2.61 - 3.91: 131 3.91 - 5.22: 23 5.22 - 6.52: 12 Bond angle restraints: 10027 Sorted by residual: angle pdb=" N LYS A 178 " pdb=" CA LYS A 178 " pdb=" C LYS A 178 " ideal model delta sigma weight residual 111.07 117.48 -6.41 1.07e+00 8.73e-01 3.59e+01 angle pdb=" N GLU A 84 " pdb=" CA GLU A 84 " pdb=" C GLU A 84 " ideal model delta sigma weight residual 111.07 117.33 -6.26 1.07e+00 8.73e-01 3.42e+01 angle pdb=" N GLU A 582 " pdb=" CA GLU A 582 " pdb=" C GLU A 582 " ideal model delta sigma weight residual 113.55 107.49 6.06 1.26e+00 6.30e-01 2.31e+01 angle pdb=" O4' DA D 10 " pdb=" C4' DA D 10 " pdb=" C3' DA D 10 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DA D 14 " pdb=" C4' DA D 14 " pdb=" C3' DA D 14 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 10022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 3810 35.75 - 71.50: 412 71.50 - 107.25: 18 107.25 - 143.01: 4 143.01 - 178.76: 7 Dihedral angle restraints: 4251 sinusoidal: 2567 harmonic: 1684 Sorted by residual: dihedral pdb=" O4' C B 5 " pdb=" C1' C B 5 " pdb=" N1 C B 5 " pdb=" C2 C B 5 " ideal model delta sinusoidal sigma weight residual 200.00 36.87 163.13 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' C B 1 " pdb=" C1' C B 1 " pdb=" N1 C B 1 " pdb=" C2 C B 1 " ideal model delta sinusoidal sigma weight residual 232.00 53.24 178.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B -25 " pdb=" C1' U B -25 " pdb=" N1 U B -25 " pdb=" C2 U B -25 " ideal model delta sinusoidal sigma weight residual -128.00 43.42 -171.42 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 4248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 884 0.050 - 0.101: 154 0.101 - 0.151: 87 0.151 - 0.202: 7 0.202 - 0.252: 2 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CA GLU A 84 " pdb=" N GLU A 84 " pdb=" C GLU A 84 " pdb=" CB GLU A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA TYR A 528 " pdb=" N TYR A 528 " pdb=" C TYR A 528 " pdb=" CB TYR A 528 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C3' DC D 4 " pdb=" C4' DC D 4 " pdb=" O3' DC D 4 " pdb=" C2' DC D 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1131 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT D -2 " 0.031 2.00e-02 2.50e+03 1.44e-02 5.19e+00 pdb=" N1 DT D -2 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT D -2 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT D -2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT D -2 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT D -2 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT D -2 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DT D -2 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT D -2 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT D -2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 201 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C GLN A 201 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN A 201 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 202 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -15 " -0.027 2.00e-02 2.50e+03 1.37e-02 4.25e+00 pdb=" N1 C B -15 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C B -15 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B -15 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C B -15 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B -15 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B -15 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C B -15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -15 " 0.006 2.00e-02 2.50e+03 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 102 2.62 - 3.19: 5527 3.19 - 3.76: 10926 3.76 - 4.33: 14528 4.33 - 4.90: 22961 Nonbonded interactions: 54044 Sorted by model distance: nonbonded pdb=" ND2 ASN A 327 " pdb="MG MG A 701 " model vdw 2.053 2.250 nonbonded pdb=" O ASP A 186 " pdb=" OD1 ASP A 186 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP A 581 " pdb="MG MG A 701 " model vdw 2.182 2.170 nonbonded pdb=" OD2 ASP A 373 " pdb=" O2' U B 12 " model vdw 2.229 3.040 nonbonded pdb=" O SER A 281 " pdb=" OG SER A 281 " model vdw 2.245 3.040 ... (remaining 54039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.005 0.063 7087 Z= 0.401 Angle : 0.762 6.521 10027 Z= 0.625 Chirality : 0.052 0.252 1134 Planarity : 0.003 0.031 943 Dihedral : 24.500 178.756 3163 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.21 % Allowed : 18.03 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.36), residues: 579 helix: 3.02 (0.30), residues: 295 sheet: 0.25 (0.56), residues: 90 loop : -1.44 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.022 0.001 TYR A 166 PHE 0.014 0.001 PHE A 256 TRP 0.013 0.002 TRP A 163 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.40 ( 7087) covalent geometry : angle 0.76179 / 0.63 (10027) hydrogen bonds : bond 0.15270 / 10.69 ( 347) hydrogen bonds : angle 5.41913 / 4.00 ( 971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.193 Fit side-chains REVERT: A 92 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7127 (tpp-160) REVERT: A 98 ARG cc_start: 0.3562 (ttm110) cc_final: 0.3349 (ttm170) REVERT: A 135 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 506 ARG cc_start: 0.6361 (mtp-110) cc_final: 0.5543 (mtp85) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.1788 time to fit residues: 10.9801 Evaluate side-chains 42 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112573 restraints weight = 9641.880| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.43 r_work: 0.3207 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7087 Z= 0.259 Angle : 0.670 7.459 10027 Z= 0.375 Chirality : 0.047 0.260 1134 Planarity : 0.005 0.035 943 Dihedral : 26.478 178.354 2029 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.07 % Allowed : 18.45 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.36), residues: 579 helix: 2.81 (0.29), residues: 302 sheet: 0.12 (0.54), residues: 95 loop : -1.80 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 452 TYR 0.029 0.002 TYR A 166 PHE 0.024 0.003 PHE A 256 TRP 0.013 0.002 TRP A 330 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.26 ( 7087) covalent geometry : angle 0.67050 / 0.37 (10027) hydrogen bonds : bond 0.07825 / 5.43 ( 347) hydrogen bonds : angle 4.15794 / 3.12 ( 971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.203 Fit side-chains REVERT: A 92 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7169 (tpp-160) REVERT: A 135 GLU cc_start: 0.8630 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 150 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: A 506 ARG cc_start: 0.6608 (mtp-110) cc_final: 0.5930 (mtp85) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1520 time to fit residues: 8.9244 Evaluate side-chains 47 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [63, 26, 62, 51, 60, 20, 19, 0, 58, 9, 52] chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116065 restraints weight = 9527.877| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.52 r_work: 0.3255 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7087 Z= 0.139 Angle : 0.532 6.505 10027 Z= 0.311 Chirality : 0.040 0.264 1134 Planarity : 0.003 0.032 943 Dihedral : 26.427 177.913 2029 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.72 % Allowed : 18.24 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.36), residues: 579 helix: 3.26 (0.29), residues: 301 sheet: 0.44 (0.57), residues: 93 loop : -1.65 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.021 0.001 TYR A 166 PHE 0.014 0.001 PHE A 256 TRP 0.014 0.002 TRP A 163 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 ( 7087) covalent geometry : angle 0.53236 / 0.31 (10027) hydrogen bonds : bond 0.05968 / 4.23 ( 347) hydrogen bonds : angle 3.76346 / 2.83 ( 971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7139 (tpp-160) REVERT: A 135 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 506 ARG cc_start: 0.6611 (mtp-110) cc_final: 0.6144 (mtp85) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.1455 time to fit residues: 9.0211 Evaluate side-chains 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [5, 57, 49, 1, 39, 24, 64, 11, 31, 44, 29] chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112806 restraints weight = 9607.217| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.50 r_work: 0.3211 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7087 Z= 0.193 Angle : 0.586 6.853 10027 Z= 0.333 Chirality : 0.043 0.262 1134 Planarity : 0.004 0.035 943 Dihedral : 26.393 178.067 2029 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.72 % Allowed : 18.67 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.36), residues: 579 helix: 3.18 (0.29), residues: 302 sheet: 0.26 (0.57), residues: 95 loop : -1.78 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 452 TYR 0.024 0.002 TYR A 166 PHE 0.019 0.002 PHE A 256 TRP 0.013 0.002 TRP A 163 HIS 0.003 0.001 HIS A 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 ( 7087) covalent geometry : angle 0.58595 / 0.33 (10027) hydrogen bonds : bond 0.06780 / 4.75 ( 347) hydrogen bonds : angle 3.76671 / 2.82 ( 971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7183 (tpp-160) REVERT: A 135 GLU cc_start: 0.8603 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 506 ARG cc_start: 0.6736 (mtp-110) cc_final: 0.6204 (mtp85) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1597 time to fit residues: 8.8108 Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [35, 15, 41, 58, 47, 57, 30, 3, 55, 33, 46] chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114677 restraints weight = 9651.204| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.45 r_work: 0.3237 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7087 Z= 0.156 Angle : 0.542 6.572 10027 Z= 0.314 Chirality : 0.041 0.262 1134 Planarity : 0.004 0.034 943 Dihedral : 26.351 177.804 2029 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.50 % Allowed : 19.53 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.36), residues: 579 helix: 3.31 (0.28), residues: 301 sheet: 0.22 (0.57), residues: 95 loop : -1.75 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.022 0.001 TYR A 166 PHE 0.016 0.002 PHE A 256 TRP 0.014 0.002 TRP A 163 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 7087) covalent geometry : angle 0.54238 / 0.31 (10027) hydrogen bonds : bond 0.06127 / 4.34 ( 347) hydrogen bonds : angle 3.65533 / 2.74 ( 971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7256 (tpp-160) REVERT: A 135 GLU cc_start: 0.8590 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 506 ARG cc_start: 0.6713 (mtp-110) cc_final: 0.6212 (mtp85) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.1477 time to fit residues: 8.0129 Evaluate side-chains 44 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [12, 50, 56, 63, 58, 5, 57, 59, 54, 27, 49] chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.0000 chunk 49 optimal weight: 3.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115666 restraints weight = 9596.633| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.45 r_work: 0.3227 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7087 Z= 0.138 Angle : 0.514 6.582 10027 Z= 0.300 Chirality : 0.040 0.261 1134 Planarity : 0.003 0.036 943 Dihedral : 26.293 178.293 2029 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 19.53 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.36), residues: 579 helix: 3.44 (0.28), residues: 301 sheet: 0.46 (0.58), residues: 93 loop : -1.73 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 179 TYR 0.022 0.001 TYR A 166 PHE 0.015 0.001 PHE A 256 TRP 0.014 0.002 TRP A 163 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 ( 7087) covalent geometry : angle 0.51431 / 0.30 (10027) hydrogen bonds : bond 0.05599 / 3.97 ( 347) hydrogen bonds : angle 3.51720 / 2.64 ( 971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7191 (tpp-160) REVERT: A 135 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 506 ARG cc_start: 0.6671 (mtp-110) cc_final: 0.6178 (mtp85) outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 0.1529 time to fit residues: 7.8077 Evaluate side-chains 44 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [8, 34, 48, 32, 63, 36, 65, 60, 24, 45, 20] chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111855 restraints weight = 9518.310| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.43 r_work: 0.3195 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7087 Z= 0.237 Angle : 0.620 6.816 10027 Z= 0.348 Chirality : 0.045 0.267 1134 Planarity : 0.005 0.035 943 Dihedral : 26.353 178.028 2029 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.15 % Allowed : 19.53 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.36), residues: 579 helix: 3.14 (0.29), residues: 301 sheet: 0.15 (0.57), residues: 95 loop : -1.87 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 452 TYR 0.027 0.002 TYR A 166 PHE 0.022 0.003 PHE A 256 TRP 0.012 0.002 TRP A 163 HIS 0.003 0.001 HIS A 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 ( 7087) covalent geometry : angle 0.62000 / 0.35 (10027) hydrogen bonds : bond 0.07241 / 5.05 ( 347) hydrogen bonds : angle 3.76183 / 2.81 ( 971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7264 (tpp-160) REVERT: A 150 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 262 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8234 (ttp-170) REVERT: A 506 ARG cc_start: 0.6760 (mtp-110) cc_final: 0.6266 (mtp85) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.1493 time to fit residues: 8.1603 Evaluate side-chains 47 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [13, 18, 24, 19, 47, 37, 59, 43, 62, 49, 30] chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112594 restraints weight = 9669.501| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.53 r_work: 0.3199 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7087 Z= 0.175 Angle : 0.561 6.686 10027 Z= 0.322 Chirality : 0.042 0.266 1134 Planarity : 0.004 0.034 943 Dihedral : 26.341 177.364 2029 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.50 % Allowed : 20.17 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.36), residues: 579 helix: 3.25 (0.28), residues: 300 sheet: 0.18 (0.57), residues: 95 loop : -1.84 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.021 0.002 TYR A 166 PHE 0.017 0.002 PHE A 256 TRP 0.014 0.002 TRP A 163 HIS 0.003 0.001 HIS A 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 ( 7087) covalent geometry : angle 0.56093 / 0.32 (10027) hydrogen bonds : bond 0.06474 / 4.58 ( 347) hydrogen bonds : angle 3.68358 / 2.76 ( 971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7205 (tpp-160) REVERT: A 262 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8123 (ttp-170) REVERT: A 506 ARG cc_start: 0.6703 (mtp-110) cc_final: 0.6169 (mtp85) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.1613 time to fit residues: 8.3123 Evaluate side-chains 46 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [52, 36, 24, 44, 48, 59, 47, 39, 14, 32, 33] chunk 52 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114762 restraints weight = 9580.387| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.44 r_work: 0.3236 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7087 Z= 0.150 Angle : 0.527 6.602 10027 Z= 0.306 Chirality : 0.040 0.265 1134 Planarity : 0.003 0.033 943 Dihedral : 26.306 177.986 2029 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.29 % Allowed : 20.39 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.36), residues: 579 helix: 3.41 (0.28), residues: 300 sheet: 0.38 (0.57), residues: 93 loop : -1.77 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 179 TYR 0.021 0.001 TYR A 166 PHE 0.016 0.002 PHE A 256 TRP 0.016 0.002 TRP A 163 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 ( 7087) covalent geometry : angle 0.52731 / 0.31 (10027) hydrogen bonds : bond 0.05900 / 4.19 ( 347) hydrogen bonds : angle 3.56591 / 2.67 ( 971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7273 (tpp-160) REVERT: A 135 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 499 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8217 (ttm170) REVERT: A 506 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6184 (mtp85) outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 0.1627 time to fit residues: 8.3850 Evaluate side-chains 46 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [16, 24, 30, 26, 25, 50, 31, 6, 43, 44, 3] chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115168 restraints weight = 9530.987| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.44 r_work: 0.3228 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7087 Z= 0.139 Angle : 0.521 6.530 10027 Z= 0.303 Chirality : 0.040 0.265 1134 Planarity : 0.003 0.033 943 Dihedral : 26.303 178.013 2029 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.29 % Allowed : 20.17 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.36), residues: 579 helix: 3.46 (0.28), residues: 300 sheet: 0.40 (0.57), residues: 93 loop : -1.75 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.021 0.001 TYR A 166 PHE 0.015 0.001 PHE A 256 TRP 0.015 0.002 TRP A 163 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 ( 7087) covalent geometry : angle 0.52120 / 0.30 (10027) hydrogen bonds : bond 0.05828 / 4.14 ( 347) hydrogen bonds : angle 3.54385 / 2.66 ( 971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7300 (tpm170) REVERT: A 135 GLU cc_start: 0.8571 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 499 ARG cc_start: 0.8611 (ttm170) cc_final: 0.8187 (ttm170) REVERT: A 506 ARG cc_start: 0.6666 (mtp-110) cc_final: 0.6161 (mtp85) outliers start: 6 outliers final: 6 residues processed: 42 average time/residue: 0.1609 time to fit residues: 8.0524 Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 523 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [10, 12, 33, 43, 55, 36, 25, 9, 8, 32, 52] chunk 10 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114946 restraints weight = 9525.270| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.44 r_work: 0.3241 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7087 Z= 0.147 Angle : 0.525 6.569 10027 Z= 0.304 Chirality : 0.040 0.266 1134 Planarity : 0.003 0.034 943 Dihedral : 26.307 178.124 2029 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.50 % Allowed : 19.96 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.36), residues: 579 helix: 3.43 (0.28), residues: 300 sheet: 0.42 (0.57), residues: 93 loop : -1.75 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.021 0.001 TYR A 166 PHE 0.016 0.002 PHE A 256 TRP 0.015 0.002 TRP A 163 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 7087) covalent geometry : angle 0.52504 / 0.30 (10027) hydrogen bonds : bond 0.05859 / 4.16 ( 347) hydrogen bonds : angle 3.54198 / 2.66 ( 971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.35 seconds wall clock time: 27 minutes 59.22 seconds (1679.22 seconds total)