Starting phenix.real_space_refine on Sat Jul 4 04:45:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pth_17871/07_2026/8pth_17871.map" } resolution = 2.73 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 27 5.49 5 S 54 5.16 5 C 5715 2.51 5 N 1629 2.21 5 O 1819 1.98 5 H 8991 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 18236 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7856 Classifications: {'peptide': 509} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2868 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 47.327 53.573 19.817 1.00 43.06 S ATOM 4472 SG CYS A 282 45.157 52.027 16.924 1.00 58.28 S Time building chain proxies: 3.01, per 1000 atoms: 0.17 Number of scatterers: 18236 At special positions: 0 Unit cell: (89.88, 94.92, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 27 15.00 O 1819 8.00 N 1629 7.00 C 5715 6.00 H 8991 1.00 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: 1.76 Conformation dependent library (CDL) restraints added in 622.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " Number of angles added : 1 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 13 sheets defined 43.4% alpha, 11.9% beta 7 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.661A pdb=" N CYS A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.600A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.530A pdb=" N GLU A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.404A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.598A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.875A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.696A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 161 through 183 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.737A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.854A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.751A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.006A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.393A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.660A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.660A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.869A pdb=" N CYS B 142 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 213 removed outlier: 3.534A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 385 through 388 removed outlier: 6.714A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8961 1.03 - 1.23: 40 1.23 - 1.42: 3972 1.42 - 1.61: 5420 1.61 - 1.81: 76 Bond restraints: 18469 Sorted by residual: bond pdb=" N LYS C 40 " pdb=" CA LYS C 40 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.28e-02 6.10e+03 6.66e+00 bond pdb=" N LYS C 40 " pdb=" H LYS C 40 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" CA LYS C 40 " pdb=" C LYS C 40 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.40e-02 5.10e+03 1.02e+00 bond pdb=" C LYS C 40 " pdb=" O LYS C 40 " ideal model delta sigma weight residual 1.235 1.247 -0.012 1.26e-02 6.30e+03 9.30e-01 bond pdb=" NZ LYS C 40 " pdb=" HZ2 LYS C 40 " ideal model delta sigma weight residual 0.890 0.908 -0.018 2.00e-02 2.50e+03 7.83e-01 ... (remaining 18464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 32740 1.41 - 2.81: 561 2.81 - 4.22: 60 4.22 - 5.63: 0 5.63 - 7.03: 1 Bond angle restraints: 33362 Sorted by residual: angle pdb=" C LEU A 300 " pdb=" N ASP A 301 " pdb=" CA ASP A 301 " ideal model delta sigma weight residual 120.49 127.52 -7.03 1.42e+00 4.96e-01 2.45e+01 angle pdb=" CA LYS C 40 " pdb=" C LYS C 40 " pdb=" O LYS C 40 " ideal model delta sigma weight residual 120.80 117.99 2.81 1.08e+00 8.57e-01 6.78e+00 angle pdb=" CB LYS C 25 " pdb=" CG LYS C 25 " pdb=" CD LYS C 25 " ideal model delta sigma weight residual 111.30 115.15 -3.85 2.30e+00 1.89e-01 2.80e+00 angle pdb=" C ARG C 39 " pdb=" N LYS C 40 " pdb=" CA LYS C 40 " ideal model delta sigma weight residual 121.26 123.90 -2.64 1.59e+00 3.96e-01 2.75e+00 angle pdb=" C SER B 160 " pdb=" N HIS B 161 " pdb=" CA HIS B 161 " ideal model delta sigma weight residual 120.68 123.19 -2.51 1.52e+00 4.33e-01 2.73e+00 ... (remaining 33357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7622 17.91 - 35.81: 710 35.81 - 53.72: 235 53.72 - 71.63: 76 71.63 - 89.53: 18 Dihedral angle restraints: 8661 sinusoidal: 4944 harmonic: 3717 Sorted by residual: dihedral pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " pdb=" CD GLU B 72 " pdb=" OE1 GLU B 72 " ideal model delta sinusoidal sigma weight residual 0.00 89.53 -89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 248 " pdb=" CD ARG B 248 " pdb=" NE ARG B 248 " pdb=" CZ ARG B 248 " ideal model delta sinusoidal sigma weight residual 180.00 -135.33 -44.67 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " pdb=" CD GLU B 29 " pdb=" OE1 GLU B 29 " ideal model delta sinusoidal sigma weight residual 0.00 88.95 -88.95 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 947 0.027 - 0.053: 371 0.053 - 0.080: 78 0.080 - 0.106: 52 0.106 - 0.133: 26 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 275 " pdb=" N VAL A 275 " pdb=" C VAL A 275 " pdb=" CB VAL A 275 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL B 86 " pdb=" N VAL B 86 " pdb=" C VAL B 86 " pdb=" CB VAL B 86 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1471 not shown) Planarity restraints: 2629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 301 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 302 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 429 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 430 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.018 2.00e-02 2.50e+03 7.22e-03 1.69e+00 pdb=" N9 A V 4 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" H8 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " -0.002 2.00e-02 2.50e+03 ... (remaining 2626 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.02: 173 2.02 - 2.66: 25960 2.66 - 3.31: 53063 3.31 - 3.95: 70121 3.95 - 4.60: 109135 Nonbonded interactions: 258452 Sorted by model distance: nonbonded pdb=" HB2 ALA A 268 " pdb="HD13 LEU C 31 " model vdw 1.375 2.440 nonbonded pdb=" OG1 THR B 97 " pdb=" HE2 HIS C 22 " model vdw 1.598 2.450 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.605 2.450 nonbonded pdb="HH12 ARG A 24 " pdb=" OE2 GLU A 85 " model vdw 1.611 2.450 nonbonded pdb=" H21 G D 28 " pdb=" O2 C V 13 " model vdw 1.613 2.450 ... (remaining 258447 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: 1.620 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: 0.070 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9482 Z= 0.099 Angle : 0.438 7.033 12926 Z= 0.231 Chirality : 0.035 0.133 1474 Planarity : 0.003 0.038 1563 Dihedral : 17.539 89.534 3689 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.88 % Allowed : 20.23 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1094 helix: 2.19 (0.25), residues: 438 sheet: -0.49 (0.56), residues: 92 loop : -0.39 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 83 TYR 0.009 0.001 TYR A 403 PHE 0.006 0.001 PHE C 44 TRP 0.003 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 9478) covalent geometry : angle 0.43825 / 0.23 (12925) hydrogen bonds : bond 0.12128 / 8.33 ( 401) hydrogen bonds : angle 4.69309 / 3.24 ( 1108) metal coordination : bond 0.00146 / 0.07 ( 4) metal coordination : angle 0.72439 / 0.38 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.515 Fit side-chains REVERT: B 327 LEU cc_start: 0.8461 (tt) cc_final: 0.7966 (pp) outliers start: 18 outliers final: 16 residues processed: 121 average time/residue: 1.1552 time to fit residues: 150.8372 Evaluate side-chains 112 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 155 GLN B 56 ASN B 501 GLN C 128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.082382 restraints weight = 34294.545| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.72 r_work: 0.2785 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9482 Z= 0.288 Angle : 0.571 6.357 12926 Z= 0.304 Chirality : 0.041 0.151 1474 Planarity : 0.005 0.060 1563 Dihedral : 10.993 73.807 1590 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.02 % Allowed : 18.87 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1094 helix: 1.80 (0.25), residues: 442 sheet: -1.01 (0.52), residues: 100 loop : -0.50 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 83 TYR 0.018 0.002 TYR A 403 PHE 0.017 0.002 PHE C 44 TRP 0.007 0.001 TRP B 2 HIS 0.008 0.002 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.29 ( 9478) covalent geometry : angle 0.56988 / 0.30 (12925) hydrogen bonds : bond 0.06892 / 4.94 ( 401) hydrogen bonds : angle 4.20833 / 2.95 ( 1108) metal coordination : bond 0.01579 / 0.79 ( 4) metal coordination : angle 3.17698 / 1.67 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.483 Fit side-chains REVERT: A 83 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: B 148 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: B 327 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8017 (pp) REVERT: C 88 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7322 (mp10) outliers start: 29 outliers final: 10 residues processed: 114 average time/residue: 1.2574 time to fit residues: 153.6768 Evaluate side-chains 111 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085106 restraints weight = 34712.398| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.72 r_work: 0.2825 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9482 Z= 0.123 Angle : 0.467 4.055 12926 Z= 0.247 Chirality : 0.036 0.146 1474 Planarity : 0.004 0.050 1563 Dihedral : 10.667 73.584 1577 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.98 % Allowed : 19.92 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1094 helix: 1.97 (0.25), residues: 442 sheet: -0.95 (0.52), residues: 100 loop : -0.42 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.013 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9478) covalent geometry : angle 0.46688 / 0.25 (12925) hydrogen bonds : bond 0.05840 / 4.19 ( 401) hydrogen bonds : angle 3.91575 / 2.75 ( 1108) metal coordination : bond 0.00306 / 0.15 ( 4) metal coordination : angle 1.13033 / 0.59 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.537 Fit side-chains REVERT: A 141 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7687 (mmt-90) REVERT: B 20 MET cc_start: 0.8346 (mtt) cc_final: 0.7932 (mtt) REVERT: B 59 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8700 (mm-30) REVERT: B 186 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: B 327 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7966 (pp) REVERT: B 397 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8672 (p0) REVERT: C 88 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7315 (mp10) outliers start: 19 outliers final: 10 residues processed: 117 average time/residue: 1.0802 time to fit residues: 136.6877 Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.081625 restraints weight = 34513.858| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.76 r_work: 0.2761 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9482 Z= 0.168 Angle : 0.487 5.019 12926 Z= 0.258 Chirality : 0.037 0.145 1474 Planarity : 0.004 0.053 1563 Dihedral : 10.629 73.728 1577 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.09 % Allowed : 20.33 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1094 helix: 1.94 (0.25), residues: 442 sheet: -1.03 (0.52), residues: 100 loop : -0.47 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 145 TYR 0.014 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9478) covalent geometry : angle 0.48631 / 0.26 (12925) hydrogen bonds : bond 0.06002 / 4.32 ( 401) hydrogen bonds : angle 3.92571 / 2.76 ( 1108) metal coordination : bond 0.00817 / 0.41 ( 4) metal coordination : angle 2.09597 / 1.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.501 Fit side-chains REVERT: A 141 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7688 (mmt-90) REVERT: B 327 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8025 (pp) REVERT: C 83 ARG cc_start: 0.6954 (tmm-80) cc_final: 0.6668 (tmm-80) REVERT: C 88 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7349 (mp10) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 1.1019 time to fit residues: 131.1763 Evaluate side-chains 117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.082921 restraints weight = 34184.617| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.76 r_work: 0.2725 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9482 Z= 0.124 Angle : 0.459 4.585 12926 Z= 0.242 Chirality : 0.036 0.144 1474 Planarity : 0.004 0.046 1563 Dihedral : 10.539 73.631 1577 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.19 % Allowed : 20.23 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1094 helix: 2.03 (0.25), residues: 442 sheet: -0.91 (0.58), residues: 88 loop : -0.46 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.013 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9478) covalent geometry : angle 0.45922 / 0.24 (12925) hydrogen bonds : bond 0.05682 / 4.09 ( 401) hydrogen bonds : angle 3.82998 / 2.70 ( 1108) metal coordination : bond 0.00341 / 0.17 ( 4) metal coordination : angle 1.38068 / 0.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7843 (mmt-90) cc_final: 0.7617 (mmt-90) REVERT: B 59 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8682 (mm-30) REVERT: B 327 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8026 (pp) REVERT: C 83 ARG cc_start: 0.6940 (tmm-80) cc_final: 0.6646 (tmm-80) outliers start: 21 outliers final: 12 residues processed: 115 average time/residue: 1.1153 time to fit residues: 138.5099 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.082418 restraints weight = 33990.303| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.74 r_work: 0.2746 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9482 Z= 0.161 Angle : 0.476 5.017 12926 Z= 0.252 Chirality : 0.037 0.144 1474 Planarity : 0.004 0.053 1563 Dihedral : 10.562 73.690 1577 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.09 % Allowed : 20.54 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1094 helix: 1.98 (0.25), residues: 442 sheet: -0.96 (0.58), residues: 88 loop : -0.48 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.014 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 9478) covalent geometry : angle 0.47587 / 0.25 (12925) hydrogen bonds : bond 0.05877 / 4.23 ( 401) hydrogen bonds : angle 3.85766 / 2.72 ( 1108) metal coordination : bond 0.00802 / 0.40 ( 4) metal coordination : angle 2.13819 / 1.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8086 (tptp) cc_final: 0.7873 (tptp) REVERT: A 141 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7657 (mmt-90) REVERT: B 327 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8103 (pp) REVERT: B 474 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8366 (m-70) REVERT: C 83 ARG cc_start: 0.6938 (tmm-80) cc_final: 0.6663 (tmm-80) REVERT: C 88 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7350 (mp10) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 1.0354 time to fit residues: 122.1032 Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 474 HIS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 90 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.084979 restraints weight = 34488.142| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.76 r_work: 0.2763 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9482 Z= 0.087 Angle : 0.439 4.092 12926 Z= 0.230 Chirality : 0.035 0.141 1474 Planarity : 0.004 0.060 1563 Dihedral : 10.417 75.766 1577 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.46 % Allowed : 20.86 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1094 helix: 2.17 (0.25), residues: 442 sheet: -0.77 (0.58), residues: 86 loop : -0.42 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.011 0.001 TYR A 403 PHE 0.005 0.001 PHE B 158 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 9478) covalent geometry : angle 0.43885 / 0.23 (12925) hydrogen bonds : bond 0.05296 / 3.81 ( 401) hydrogen bonds : angle 3.68649 / 2.60 ( 1108) metal coordination : bond 0.00317 / 0.16 ( 4) metal coordination : angle 0.52206 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8076 (pp) REVERT: B 474 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8323 (m-70) REVERT: C 83 ARG cc_start: 0.6868 (tmm-80) cc_final: 0.6574 (tmm-80) outliers start: 14 outliers final: 7 residues processed: 113 average time/residue: 1.1705 time to fit residues: 142.8667 Evaluate side-chains 113 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 474 HIS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 501 GLN B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.081618 restraints weight = 34288.012| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.75 r_work: 0.2714 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9482 Z= 0.189 Angle : 0.491 4.700 12926 Z= 0.259 Chirality : 0.038 0.143 1474 Planarity : 0.005 0.078 1563 Dihedral : 10.489 73.715 1575 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.67 % Allowed : 20.86 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1094 helix: 2.01 (0.25), residues: 442 sheet: -0.85 (0.58), residues: 86 loop : -0.49 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 33 TYR 0.014 0.001 TYR A 403 PHE 0.014 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 9478) covalent geometry : angle 0.49014 / 0.26 (12925) hydrogen bonds : bond 0.05936 / 4.28 ( 401) hydrogen bonds : angle 3.83522 / 2.71 ( 1108) metal coordination : bond 0.01026 / 0.51 ( 4) metal coordination : angle 2.38974 / 1.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 59 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 204 GLU cc_start: 0.8372 (tt0) cc_final: 0.8115 (tp30) REVERT: B 327 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8159 (pp) REVERT: B 474 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8363 (m-70) REVERT: C 83 ARG cc_start: 0.6924 (tmm-80) cc_final: 0.6650 (tmm-80) REVERT: C 88 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7372 (mp10) outliers start: 16 outliers final: 7 residues processed: 106 average time/residue: 1.0752 time to fit residues: 123.2456 Evaluate side-chains 113 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 474 HIS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 87 GLN B 501 GLN B 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.083728 restraints weight = 34222.401| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.74 r_work: 0.2734 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9482 Z= 0.114 Angle : 0.458 4.579 12926 Z= 0.241 Chirality : 0.036 0.143 1474 Planarity : 0.004 0.069 1563 Dihedral : 10.426 74.320 1575 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.67 % Allowed : 20.75 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1094 helix: 2.08 (0.25), residues: 442 sheet: -0.81 (0.58), residues: 86 loop : -0.45 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 9478) covalent geometry : angle 0.45799 / 0.24 (12925) hydrogen bonds : bond 0.05542 / 3.99 ( 401) hydrogen bonds : angle 3.74594 / 2.64 ( 1108) metal coordination : bond 0.00266 / 0.13 ( 4) metal coordination : angle 1.38115 / 0.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.460 Fit side-chains REVERT: B 117 THR cc_start: 0.8865 (m) cc_final: 0.8547 (m) REVERT: B 204 GLU cc_start: 0.8356 (tt0) cc_final: 0.8080 (tp30) REVERT: B 327 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8139 (pp) REVERT: C 83 ARG cc_start: 0.6837 (tmm-80) cc_final: 0.6546 (tmm-80) REVERT: C 111 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6589 (mmm160) outliers start: 16 outliers final: 8 residues processed: 108 average time/residue: 1.0384 time to fit residues: 121.1987 Evaluate side-chains 109 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 111 ARG Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 87 GLN B 501 GLN B 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.083447 restraints weight = 34297.564| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.76 r_work: 0.2763 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9482 Z= 0.114 Angle : 0.459 4.584 12926 Z= 0.242 Chirality : 0.036 0.142 1474 Planarity : 0.004 0.067 1563 Dihedral : 10.408 74.757 1575 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.36 % Allowed : 21.17 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1094 helix: 2.11 (0.25), residues: 442 sheet: -0.81 (0.58), residues: 86 loop : -0.45 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.008 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9478) covalent geometry : angle 0.45879 / 0.24 (12925) hydrogen bonds : bond 0.05500 / 3.96 ( 401) hydrogen bonds : angle 3.73239 / 2.64 ( 1108) metal coordination : bond 0.00298 / 0.15 ( 4) metal coordination : angle 1.42467 / 0.75 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: B 117 THR cc_start: 0.8879 (m) cc_final: 0.8568 (m) REVERT: B 327 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8179 (pp) REVERT: B 339 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: C 83 ARG cc_start: 0.6853 (tmm-80) cc_final: 0.6568 (tmm-80) REVERT: C 111 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6589 (mmm160) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 1.0167 time to fit residues: 116.8459 Evaluate side-chains 113 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 111 ARG Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 87 GLN B 501 GLN B 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.083357 restraints weight = 34394.414| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.76 r_work: 0.2733 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9482 Z= 0.115 Angle : 0.454 4.053 12926 Z= 0.239 Chirality : 0.036 0.141 1474 Planarity : 0.004 0.064 1563 Dihedral : 10.387 74.904 1575 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.36 % Allowed : 21.17 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1094 helix: 2.13 (0.25), residues: 442 sheet: -0.85 (0.58), residues: 86 loop : -0.44 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.008 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 9478) covalent geometry : angle 0.45423 / 0.24 (12925) hydrogen bonds : bond 0.05448 / 3.92 ( 401) hydrogen bonds : angle 3.69805 / 2.61 ( 1108) metal coordination : bond 0.00331 / 0.17 ( 4) metal coordination : angle 1.44876 / 0.76 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5759.60 seconds wall clock time: 98 minutes 15.94 seconds (5895.94 seconds total)