Starting phenix.real_space_refine on Thu Jul 2 03:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k88_36947/07_2026/8k88_36947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k88_36947/07_2026/8k88_36947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k88_36947/07_2026/8k88_36947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k88_36947/07_2026/8k88_36947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k88_36947/07_2026/8k88_36947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k88_36947/07_2026/8k88_36947.map" } resolution = 2.6 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= 0.005 sd= 0.050 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 44 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4124 2.51 5 N 1150 2.21 5 O 1345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6686 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} 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: 1.24, per 1000 atoms: 0.19 Number of scatterers: 6686 At special positions: 0 Unit cell: (74.6512, 90.2876, 107.437, 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 22 16.00 P 44 15.00 Mg 1 11.99 O 1345 8.00 N 1150 7.00 C 4124 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: 0.60 Conformation dependent library (CDL) restraints added in 279.4 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.7% alpha, 24.1% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.883A pdb=" N CYS A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.735A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.949A pdb=" N GLY A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.705A pdb=" N ARG A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 4.920A pdb=" N LYS A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.891A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.680A pdb=" N VAL A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.634A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 4.266A pdb=" N THR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.024A pdb=" N VAL A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.601A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 513 through 519 removed outlier: 4.968A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.156A pdb=" N LEU A 331 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 223 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 306 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 225 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.324A pdb=" N CYS A 107 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 54 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.190A pdb=" N ARG A 51 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 147 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA A 53 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR A 149 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 55 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 146 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 183 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 148 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 3.624A pdb=" N ALA A 355 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.262A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.739A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 382 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N ARG B 344 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 343 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR B 403 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS B 345 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN B 401 " --> pdb=" O CYS B 345 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 347 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 399 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 349 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 556 through 561 271 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1887 1.34 - 1.45: 1374 1.45 - 1.57: 3555 1.57 - 1.69: 86 1.69 - 1.81: 32 Bond restraints: 6934 Sorted by residual: bond pdb=" C3' DA C 15 " pdb=" C2' DA C 15 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DT C 23 " pdb=" C2' DT C 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.82e+00 bond pdb=" C3' DC C 20 " pdb=" C2' DC C 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.39e+00 bond pdb=" C3' DC C 21 " pdb=" C2' DC C 21 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.34e+00 bond pdb=" C3' DC C 9 " pdb=" C2' DC C 9 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.14e+00 ... (remaining 6929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9366 1.78 - 3.55: 200 3.55 - 5.33: 20 5.33 - 7.10: 6 7.10 - 8.88: 2 Bond angle restraints: 9594 Sorted by residual: angle pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sigma weight residual 117.70 123.50 -5.80 1.20e+00 6.94e-01 2.34e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT C 24 " pdb=" C4 DT C 24 " pdb=" O4 DT C 24 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" C1' G D 15 " pdb=" N9 G D 15 " pdb=" C4 G D 15 " ideal model delta sigma weight residual 126.50 131.84 -5.34 1.30e+00 5.92e-01 1.69e+01 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 3828 34.39 - 68.77: 273 68.77 - 103.16: 14 103.16 - 137.54: 1 137.54 - 171.93: 1 Dihedral angle restraints: 4117 sinusoidal: 2007 harmonic: 2110 Sorted by residual: dihedral pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sinusoidal sigma weight residual -160.00 11.93 -171.93 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " pdb=" NE ARG A 69 " pdb=" CZ ARG A 69 " ideal model delta sinusoidal sigma weight residual -90.00 -37.10 -52.90 2 1.50e+01 4.44e-03 1.36e+01 dihedral pdb=" C4' DT C 13 " pdb=" C3' DT C 13 " pdb=" O3' DT C 13 " pdb=" P DA C 14 " ideal model delta sinusoidal sigma weight residual 220.00 103.43 116.57 1 3.50e+01 8.16e-04 1.13e+01 ... (remaining 4114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 716 0.032 - 0.064: 246 0.064 - 0.096: 61 0.096 - 0.128: 48 0.128 - 0.160: 3 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C3' DT C 24 " pdb=" C4' DT C 24 " pdb=" O3' DT C 24 " pdb=" C2' DT C 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" C1' G D 15 " pdb=" O4' G D 15 " pdb=" C2' G D 15 " pdb=" N9 G D 15 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1071 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 389 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 390 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.68e+00 pdb=" N9 A D 4 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 401 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 402 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.029 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 44 2.56 - 3.14: 4837 3.14 - 3.73: 10670 3.73 - 4.31: 15184 4.31 - 4.90: 24623 Nonbonded interactions: 55358 Sorted by model distance: nonbonded pdb=" OXT MET A 473 " pdb="MG MG A 501 " model vdw 1.973 2.170 nonbonded pdb=" OP1 A D 3 " pdb="MG MG A 501 " model vdw 1.987 2.170 nonbonded pdb=" OP2 A D 1 " pdb="MG MG A 501 " model vdw 2.070 2.170 nonbonded pdb=" O THR A 242 " pdb=" OG1 THR A 262 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 195 " pdb=" ND2 ASN A 436 " model vdw 2.212 3.120 ... (remaining 55353 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: 1.600 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.730 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:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.003 0.034 6934 Z= 0.232 Angle : 0.607 8.877 9594 Z= 0.417 Chirality : 0.040 0.160 1074 Planarity : 0.005 0.065 1076 Dihedral : 20.288 171.926 2761 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.96 % Allowed : 27.97 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.49 (0.32), residues: 722 helix: 2.27 (0.35), residues: 221 sheet: 0.96 (0.40), residues: 180 loop : 0.16 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 529 TYR 0.022 0.001 TYR A 341 PHE 0.008 0.001 PHE A 137 TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.23 ( 6934) covalent geometry : angle 0.60684 / 0.42 ( 9594) hydrogen bonds : bond 0.14900 / 15.87 ( 297) hydrogen bonds : angle 6.07695 / 7.33 ( 811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.172 Fit side-chains REVERT: A 156 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8197 (ptmm) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.5317 time to fit residues: 107.0115 Evaluate side-chains 188 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106675 restraints weight = 9145.682| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.59 r_work: 0.3345 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6934 Z= 0.144 Angle : 0.549 6.828 9594 Z= 0.305 Chirality : 0.041 0.162 1074 Planarity : 0.005 0.051 1076 Dihedral : 18.509 174.274 1379 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.73 % Allowed : 24.76 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.47 (0.32), residues: 722 helix: 2.38 (0.35), residues: 222 sheet: 0.88 (0.40), residues: 180 loop : 0.09 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 529 TYR 0.014 0.001 TYR A 366 PHE 0.017 0.001 PHE A 304 TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6934) covalent geometry : angle 0.54888 / 0.31 ( 9594) hydrogen bonds : bond 0.04280 / 4.87 ( 297) hydrogen bonds : angle 4.57836 / 5.56 ( 811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.214 Fit side-chains REVERT: B 504 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7448 (mmm) outliers start: 17 outliers final: 11 residues processed: 192 average time/residue: 0.6443 time to fit residues: 128.7828 Evaluate side-chains 192 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 5 optimal weight: 0.0980 chunk 50 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107621 restraints weight = 9010.522| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.58 r_work: 0.3361 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6934 Z= 0.114 Angle : 0.507 5.823 9594 Z= 0.285 Chirality : 0.040 0.147 1074 Planarity : 0.005 0.045 1076 Dihedral : 18.467 172.929 1371 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.05 % Allowed : 23.31 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 (0.32), residues: 722 helix: 2.41 (0.35), residues: 222 sheet: 0.88 (0.41), residues: 180 loop : 0.10 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.013 0.001 TYR A 366 PHE 0.016 0.001 PHE A 143 TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 6934) covalent geometry : angle 0.50701 / 0.28 ( 9594) hydrogen bonds : bond 0.03851 / 4.42 ( 297) hydrogen bonds : angle 4.33642 / 5.26 ( 811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.225 Fit side-chains REVERT: B 358 GLU cc_start: 0.7910 (tp30) cc_final: 0.7698 (tp30) REVERT: B 504 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7407 (mmm) outliers start: 19 outliers final: 11 residues processed: 193 average time/residue: 0.6089 time to fit residues: 122.3720 Evaluate side-chains 196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 70 optimal weight: 0.0070 chunk 74 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.117317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105896 restraints weight = 9011.346| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.57 r_work: 0.3333 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6934 Z= 0.155 Angle : 0.522 6.304 9594 Z= 0.290 Chirality : 0.041 0.169 1074 Planarity : 0.005 0.047 1076 Dihedral : 18.396 174.212 1371 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.70 % Allowed : 23.63 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.46 (0.32), residues: 722 helix: 2.41 (0.35), residues: 222 sheet: 0.85 (0.41), residues: 180 loop : 0.07 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.015 0.001 TYR A 366 PHE 0.021 0.001 PHE B 579 TRP 0.009 0.001 TRP B 502 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6934) covalent geometry : angle 0.52222 / 0.29 ( 9594) hydrogen bonds : bond 0.03831 / 4.35 ( 297) hydrogen bonds : angle 4.26317 / 5.17 ( 811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.164 Fit side-chains REVERT: B 358 GLU cc_start: 0.7962 (tp30) cc_final: 0.7749 (tp30) REVERT: B 504 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7542 (mmm) outliers start: 23 outliers final: 11 residues processed: 192 average time/residue: 0.5785 time to fit residues: 115.6484 Evaluate side-chains 195 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104294 restraints weight = 9133.995| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.59 r_work: 0.3308 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6934 Z= 0.205 Angle : 0.541 6.170 9594 Z= 0.298 Chirality : 0.042 0.172 1074 Planarity : 0.005 0.047 1076 Dihedral : 18.427 176.139 1371 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.86 % Allowed : 23.63 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.36 (0.32), residues: 722 helix: 2.32 (0.35), residues: 222 sheet: 0.79 (0.41), residues: 180 loop : 0.01 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 69 TYR 0.017 0.002 TYR A 341 PHE 0.021 0.002 PHE B 579 TRP 0.010 0.001 TRP B 502 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 6934) covalent geometry : angle 0.54105 / 0.30 ( 9594) hydrogen bonds : bond 0.04099 / 4.64 ( 297) hydrogen bonds : angle 4.31369 / 5.24 ( 811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.158 Fit side-chains REVERT: A 49 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: B 358 GLU cc_start: 0.7981 (tp30) cc_final: 0.7779 (tp30) outliers start: 24 outliers final: 12 residues processed: 193 average time/residue: 0.5497 time to fit residues: 110.4096 Evaluate side-chains 192 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104858 restraints weight = 9158.269| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.58 r_work: 0.3315 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6934 Z= 0.166 Angle : 0.524 5.939 9594 Z= 0.292 Chirality : 0.041 0.161 1074 Planarity : 0.005 0.046 1076 Dihedral : 18.434 177.137 1371 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.54 % Allowed : 23.63 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.34 (0.32), residues: 722 helix: 2.28 (0.35), residues: 222 sheet: 0.78 (0.41), residues: 180 loop : 0.02 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.014 0.001 TYR A 366 PHE 0.025 0.001 PHE B 579 TRP 0.010 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 6934) covalent geometry : angle 0.52429 / 0.29 ( 9594) hydrogen bonds : bond 0.03912 / 4.48 ( 297) hydrogen bonds : angle 4.25778 / 5.17 ( 811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.238 Fit side-chains REVERT: A 49 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8434 (pt0) outliers start: 22 outliers final: 12 residues processed: 190 average time/residue: 0.6088 time to fit residues: 120.3351 Evaluate side-chains 198 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 483 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.0020 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104373 restraints weight = 9064.079| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.57 r_work: 0.3309 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.004 0.036 6934 Z= 0.187 Angle : 0.539 6.085 9594 Z= 0.298 Chirality : 0.042 0.168 1074 Planarity : 0.005 0.046 1076 Dihedral : 18.439 178.212 1371 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.70 % Allowed : 23.63 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.32 (0.32), residues: 722 helix: 2.28 (0.35), residues: 222 sheet: 0.78 (0.41), residues: 180 loop : -0.01 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.018 0.001 TYR A 366 PHE 0.033 0.002 PHE B 579 TRP 0.010 0.001 TRP B 502 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 6934) covalent geometry : angle 0.53860 / 0.30 ( 9594) hydrogen bonds : bond 0.03977 / 4.52 ( 297) hydrogen bonds : angle 4.27660 / 5.19 ( 811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.145 Fit side-chains REVERT: A 49 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: A 293 SER cc_start: 0.8485 (p) cc_final: 0.8250 (p) outliers start: 23 outliers final: 17 residues processed: 194 average time/residue: 0.5913 time to fit residues: 119.3736 Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104230 restraints weight = 9051.112| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.55 r_work: 0.3306 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6934 Z= 0.190 Angle : 0.539 6.033 9594 Z= 0.298 Chirality : 0.042 0.168 1074 Planarity : 0.005 0.068 1076 Dihedral : 18.467 179.270 1371 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.70 % Allowed : 23.95 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.25 (0.32), residues: 722 helix: 2.22 (0.35), residues: 222 sheet: 0.71 (0.41), residues: 180 loop : -0.04 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 529 TYR 0.017 0.001 TYR A 366 PHE 0.026 0.001 PHE B 579 TRP 0.010 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 6934) covalent geometry : angle 0.53934 / 0.30 ( 9594) hydrogen bonds : bond 0.03995 / 4.55 ( 297) hydrogen bonds : angle 4.27701 / 5.19 ( 811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.194 Fit side-chains REVERT: A 49 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: A 293 SER cc_start: 0.8469 (p) cc_final: 0.8236 (p) outliers start: 23 outliers final: 18 residues processed: 196 average time/residue: 0.5634 time to fit residues: 114.9790 Evaluate side-chains 203 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104957 restraints weight = 9129.201| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.58 r_work: 0.3319 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6934 Z= 0.136 Angle : 0.526 6.169 9594 Z= 0.293 Chirality : 0.041 0.151 1074 Planarity : 0.005 0.056 1076 Dihedral : 18.471 179.988 1371 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.38 % Allowed : 24.60 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.30 (0.32), residues: 722 helix: 2.30 (0.35), residues: 222 sheet: 0.72 (0.41), residues: 180 loop : -0.02 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 62 TYR 0.012 0.001 TYR A 366 PHE 0.020 0.001 PHE A 257 TRP 0.010 0.001 TRP B 502 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 6934) covalent geometry : angle 0.52601 / 0.29 ( 9594) hydrogen bonds : bond 0.03786 / 4.37 ( 297) hydrogen bonds : angle 4.22967 / 5.12 ( 811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.153 Fit side-chains REVERT: A 49 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8406 (pt0) outliers start: 21 outliers final: 17 residues processed: 191 average time/residue: 0.5830 time to fit residues: 115.9908 Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105128 restraints weight = 9150.566| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.57 r_work: 0.3322 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6934 Z= 0.140 Angle : 0.527 6.401 9594 Z= 0.292 Chirality : 0.041 0.151 1074 Planarity : 0.005 0.051 1076 Dihedral : 18.427 178.986 1371 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.73 % Allowed : 25.72 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.34 (0.32), residues: 722 helix: 2.33 (0.35), residues: 222 sheet: 0.70 (0.41), residues: 180 loop : 0.03 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 62 TYR 0.017 0.001 TYR A 366 PHE 0.021 0.001 PHE A 257 TRP 0.009 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6934) covalent geometry : angle 0.52685 / 0.29 ( 9594) hydrogen bonds : bond 0.03716 / 4.27 ( 297) hydrogen bonds : angle 4.20929 / 5.09 ( 811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.250 Fit side-chains REVERT: A 49 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: B 576 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7974 (ttt-90) outliers start: 17 outliers final: 15 residues processed: 189 average time/residue: 0.6438 time to fit residues: 126.6500 Evaluate side-chains 199 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103835 restraints weight = 9077.473| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.56 r_work: 0.3301 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6934 Z= 0.209 Angle : 0.559 6.364 9594 Z= 0.307 Chirality : 0.043 0.178 1074 Planarity : 0.005 0.050 1076 Dihedral : 18.474 178.636 1371 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 25.08 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.23 (0.32), residues: 722 helix: 2.10 (0.35), residues: 228 sheet: 0.66 (0.40), residues: 183 loop : 0.02 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.017 0.001 TYR A 341 PHE 0.027 0.002 PHE A 257 TRP 0.010 0.001 TRP B 502 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 6934) covalent geometry : angle 0.55907 / 0.31 ( 9594) hydrogen bonds : bond 0.04059 / 4.61 ( 297) hydrogen bonds : angle 4.30060 / 5.22 ( 811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.67 seconds wall clock time: 48 minutes 57.35 seconds (2937.35 seconds total)