Starting phenix.real_space_refine on Wed Aug 5 01:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo8_61646/08_2026/9jo8_61646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo8_61646/08_2026/9jo8_61646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jo8_61646/08_2026/9jo8_61646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo8_61646/08_2026/9jo8_61646.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo8_61646/08_2026/9jo8_61646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo8_61646/08_2026/9jo8_61646.cif" } resolution = 3.0 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 974 atoms to isotropic. 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 Zn 1 6.06 5 P 66 5.49 5 S 20 5.16 5 C 4187 2.51 5 N 1268 2.21 5 O 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7001 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4664 Classifications: {'peptide': 638} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 602} Chain: "B" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 670 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 683 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 982 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 13, 'TRANS': 119} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" 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 6642 SG CYS D1373 43.099 44.783 91.658 1.00 48.68 S ATOM 6663 SG CYS D1376 46.459 44.318 93.766 1.00 72.39 S Time building chain proxies: 1.54, per 1000 atoms: 0.22 Number of scatterers: 7001 At special positions: 0 Unit cell: (86.787, 85.8227, 123.43, 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) Zn 1 29.99 S 20 16.00 P 66 15.00 O 1459 8.00 N 1268 7.00 C 4187 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: 0.43 Conformation dependent library (CDL) restraints added in 339.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D1376 " pdb="ZN ZN D1501 " - pdb=" SG CYS D1373 " pdb="ZN ZN D1501 " - pdb=" ND1 HIS D1345 " 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 70.6% alpha, 3.5% beta 2 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 removed outlier: 3.510A pdb=" N LYS A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 57 removed outlier: 4.105A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.501A pdb=" N THR A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 128 removed outlier: 7.805A pdb=" N VAL A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 170 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.715A pdb=" N VAL A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 204 removed outlier: 3.520A pdb=" N ARG A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 254 through 272 Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 288 through 304 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.632A pdb=" N ARG A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 356 through 375 Proline residue: A 369 - end of helix removed outlier: 3.732A pdb=" N HIS A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 390 through 409 Proline residue: A 403 - end of helix removed outlier: 3.674A pdb=" N HIS A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 424 through 442 Proline residue: A 437 - end of helix removed outlier: 3.539A pdb=" N GLN A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 458 through 477 Proline residue: A 471 - end of helix removed outlier: 3.819A pdb=" N HIS A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 4.462A pdb=" N HIS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 526 through 542 Proline residue: A 539 - end of helix Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 560 through 579 Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 596 through 612 Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.873A pdb=" N ASN A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 removed outlier: 3.516A pdb=" N SER A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 1341 through 1344 removed outlier: 3.767A pdb=" N GLY D1344 " --> pdb=" O VAL D1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1341 through 1344' Processing helix chain 'D' and resid 1345 through 1357 removed outlier: 3.534A pdb=" N SER D1350 " --> pdb=" O VAL D1346 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA D1351 " --> pdb=" O GLU D1347 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN D1357 " --> pdb=" O PHE D1353 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1384 removed outlier: 6.003A pdb=" N GLU D1381 " --> pdb=" O VAL D1377 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR D1382 " --> pdb=" O ASN D1378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 1291 through 1294 removed outlier: 3.532A pdb=" N LEU D1294 " --> pdb=" O TYR D1297 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1325 through 1330 removed outlier: 3.752A pdb=" N GLY D1362 " --> pdb=" O LYS D1389 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D1391 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D1392 " --> pdb=" O LYS D1410 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D1410 " --> pdb=" O VAL D1392 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1703 1.33 - 1.45: 1530 1.45 - 1.57: 3869 1.57 - 1.69: 131 1.69 - 1.81: 24 Bond restraints: 7257 Sorted by residual: bond pdb=" C GLY A 559 " pdb=" N GLY A 560 " ideal model delta sigma weight residual 1.329 1.290 0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.473 1.419 0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" C3' DG C 14 " pdb=" C2' DG C 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA C 9 " pdb=" C2' DA C 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG C 8 " pdb=" C2' DG C 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 7252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 9819 2.00 - 4.01: 274 4.01 - 6.01: 52 6.01 - 8.01: 10 8.01 - 10.02: 11 Bond angle restraints: 10166 Sorted by residual: angle pdb=" C3' DT B 29 " pdb=" O3' DT B 29 " pdb=" P DC B 30 " ideal model delta sigma weight residual 119.70 109.68 10.02 1.20e+00 6.94e-01 6.97e+01 angle pdb=" C3' DT C 3 " pdb=" O3' DT C 3 " pdb=" P DA C 4 " ideal model delta sigma weight residual 119.70 110.46 9.24 1.20e+00 6.94e-01 5.93e+01 angle pdb=" C3' DA B 26 " pdb=" O3' DA B 26 " pdb=" P DT B 27 " ideal model delta sigma weight residual 119.70 110.73 8.97 1.20e+00 6.94e-01 5.59e+01 angle pdb=" C3' DA C 2 " pdb=" O3' DA C 2 " pdb=" P DT C 3 " ideal model delta sigma weight residual 119.70 111.16 8.54 1.20e+00 6.94e-01 5.06e+01 angle pdb=" C3' DA B 28 " pdb=" O3' DA B 28 " pdb=" P DT B 29 " ideal model delta sigma weight residual 119.70 111.47 8.23 1.20e+00 6.94e-01 4.70e+01 ... (remaining 10161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 3805 35.62 - 71.24: 383 71.24 - 106.85: 12 106.85 - 142.47: 1 142.47 - 178.09: 5 Dihedral angle restraints: 4206 sinusoidal: 2048 harmonic: 2158 Sorted by residual: dihedral pdb=" C ASN A 422 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " ideal model delta harmonic sigma weight residual -122.60 -135.57 12.97 0 2.50e+00 1.60e-01 2.69e+01 dihedral pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " pdb=" O3' DT B 19 " pdb=" P DG B 20 " ideal model delta sinusoidal sigma weight residual -140.00 38.09 -178.09 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA B 25 " pdb=" C3' DA B 25 " pdb=" O3' DA B 25 " pdb=" P DA B 26 " ideal model delta sinusoidal sigma weight residual 220.00 68.34 151.66 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 4203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1190 0.124 - 0.249: 3 0.249 - 0.373: 1 0.373 - 0.498: 12 0.498 - 0.622: 2 Chirality restraints: 1208 Sorted by residual: chirality pdb=" P DG C 1 " pdb=" OP1 DG C 1 " pdb=" OP2 DG C 1 " pdb=" O5' DG C 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" P DC B 30 " pdb=" OP1 DC B 30 " pdb=" OP2 DC B 30 " pdb=" O5' DC B 30 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" P DA B 26 " pdb=" OP1 DA B 26 " pdb=" OP2 DA B 26 " pdb=" O5' DA B 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.49 2.00e-01 2.50e+01 5.95e+00 ... (remaining 1205 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 559 " -0.016 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C GLY A 559 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 559 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 560 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D1304 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO D1305 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D1305 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D1305 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 151 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ASP A 151 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP A 151 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 152 " -0.015 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 200 2.70 - 3.25: 6296 3.25 - 3.80: 10558 3.80 - 4.35: 13733 4.35 - 4.90: 22654 Nonbonded interactions: 53441 Sorted by model distance: nonbonded pdb=" OE2 GLU D1347 " pdb=" CD2 HIS D1366 " model vdw 2.151 3.260 nonbonded pdb=" O SER A 149 " pdb=" OG SER A 149 " model vdw 2.185 3.040 nonbonded pdb=" N GLU A 278 " pdb=" OE1 GLU A 278 " model vdw 2.237 3.120 nonbonded pdb=" N GLU A 346 " pdb=" OE1 GLU A 346 " model vdw 2.260 3.120 nonbonded pdb=" O SER A 455 " pdb=" OG SER A 455 " model vdw 2.273 3.040 ... (remaining 53436 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.420 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: 0.010 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 7260 Z= 0.373 Angle : 0.818 10.017 10166 Z= 0.567 Chirality : 0.067 0.622 1208 Planarity : 0.006 0.076 1104 Dihedral : 23.492 178.091 2826 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 25.62 % Favored : 74.38 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 4.17 % 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: -0.28 (0.30), residues: 767 helix: 0.38 (0.23), residues: 488 sheet: 1.49 (0.89), residues: 35 loop : -1.48 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 116 TYR 0.009 0.001 TYR D1316 PHE 0.008 0.001 PHE D1353 TRP 0.003 0.001 TRP A 82 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.37 ( 7257) covalent geometry : angle 0.81759 / 0.57 (10166) hydrogen bonds : bond 0.19256 / 13.50 ( 325) hydrogen bonds : angle 6.00404 / 4.35 ( 963) metal coordination : bond 0.00332 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.145 Fit side-chains REVERT: A 414 GLU cc_start: 0.7813 (mp0) cc_final: 0.7534 (mp0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.4829 time to fit residues: 44.2529 Evaluate side-chains 84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108608 restraints weight = 9834.439| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.45 r_work: 0.3308 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7260 Z= 0.155 Angle : 0.625 7.503 10166 Z= 0.355 Chirality : 0.046 0.247 1208 Planarity : 0.005 0.057 1104 Dihedral : 24.644 177.815 1530 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.00 % Allowed : 22.96 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.17 (0.30), residues: 767 helix: 0.48 (0.23), residues: 521 sheet: 2.22 (0.95), residues: 25 loop : -1.70 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.010 0.001 TYR D1316 PHE 0.017 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.002 0.000 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 ( 7257) covalent geometry : angle 0.62515 / 0.35 (10166) hydrogen bonds : bond 0.05222 / 3.54 ( 325) hydrogen bonds : angle 4.83453 / 3.53 ( 963) metal coordination : bond 0.00635 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.137 Fit side-chains REVERT: A 275 LEU cc_start: 0.7684 (mp) cc_final: 0.7408 (mt) REVERT: A 414 GLU cc_start: 0.7910 (mp0) cc_final: 0.7656 (mp0) REVERT: A 596 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7289 (ttpp) REVERT: D 1364 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8567 (t) outliers start: 12 outliers final: 4 residues processed: 99 average time/residue: 0.4599 time to fit residues: 47.9803 Evaluate side-chains 98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1364 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.0040 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 63.4139 > 50:) chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN D1378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106310 restraints weight = 9743.199| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.42 r_work: 0.3270 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7260 Z= 0.197 Angle : 0.651 10.404 10166 Z= 0.364 Chirality : 0.049 0.273 1208 Planarity : 0.005 0.050 1104 Dihedral : 24.769 179.853 1530 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.00 % Allowed : 21.63 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.26 (0.30), residues: 767 helix: 0.45 (0.23), residues: 524 sheet: 2.44 (0.97), residues: 23 loop : -1.86 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 6 TYR 0.014 0.001 TYR D1316 PHE 0.011 0.002 PHE D1315 TRP 0.004 0.001 TRP A 82 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 ( 7257) covalent geometry : angle 0.65075 / 0.36 (10166) hydrogen bonds : bond 0.05433 / 3.74 ( 325) hydrogen bonds : angle 4.57768 / 3.35 ( 963) metal coordination : bond 0.01053 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.217 Fit side-chains REVERT: A 344 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7066 (m) REVERT: A 414 GLU cc_start: 0.7921 (mp0) cc_final: 0.7657 (mp0) REVERT: A 576 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7153 (p) REVERT: A 596 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7310 (ttpp) REVERT: A 600 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6947 (mt-10) REVERT: D 1364 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8576 (t) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 0.4871 time to fit residues: 51.9602 Evaluate side-chains 100 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1328 VAL Chi-restraints excluded: chain D residue 1364 VAL Chi-restraints excluded: chain D residue 1408 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 58 optimal weight: 0.0870 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 495 GLN A 545 HIS D1378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108022 restraints weight = 9810.526| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.44 r_work: 0.3295 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7260 Z= 0.145 Angle : 0.602 7.925 10166 Z= 0.338 Chirality : 0.045 0.277 1208 Planarity : 0.005 0.050 1104 Dihedral : 24.838 178.070 1530 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.00 % Allowed : 22.13 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.00 (0.30), residues: 767 helix: 0.63 (0.23), residues: 522 sheet: 2.74 (0.99), residues: 23 loop : -1.73 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 6 TYR 0.008 0.001 TYR D1316 PHE 0.009 0.001 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.002 0.000 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 7257) covalent geometry : angle 0.60225 / 0.34 (10166) hydrogen bonds : bond 0.03930 / 2.70 ( 325) hydrogen bonds : angle 4.40991 / 3.23 ( 963) metal coordination : bond 0.00513 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.181 Fit side-chains REVERT: A 229 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: A 346 GLU cc_start: 0.7184 (mp0) cc_final: 0.6872 (mp0) REVERT: A 414 GLU cc_start: 0.7908 (mp0) cc_final: 0.7658 (mp0) REVERT: A 571 LEU cc_start: 0.8057 (mt) cc_final: 0.7816 (mp) REVERT: A 576 CYS cc_start: 0.7630 (t) cc_final: 0.7169 (p) REVERT: A 596 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7341 (ttpt) REVERT: D 1354 MET cc_start: 0.7827 (ttm) cc_final: 0.7595 (ttm) outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 0.5298 time to fit residues: 55.3621 Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 596 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 40 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 57 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 495 GLN A 545 HIS D1378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108009 restraints weight = 9861.561| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.44 r_work: 0.3297 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7260 Z= 0.147 Angle : 0.599 10.130 10166 Z= 0.334 Chirality : 0.045 0.288 1208 Planarity : 0.005 0.050 1104 Dihedral : 24.898 178.870 1530 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.50 % Allowed : 21.80 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.07 (0.30), residues: 767 helix: 0.68 (0.23), residues: 520 sheet: 2.86 (1.04), residues: 23 loop : -1.70 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 6 TYR 0.009 0.001 TYR D1316 PHE 0.008 0.001 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.002 0.000 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 7257) covalent geometry : angle 0.59859 / 0.33 (10166) hydrogen bonds : bond 0.03970 / 2.73 ( 325) hydrogen bonds : angle 4.31196 / 3.17 ( 963) metal coordination : bond 0.00624 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.229 Fit side-chains REVERT: A 414 GLU cc_start: 0.7913 (mp0) cc_final: 0.7671 (mp0) REVERT: A 576 CYS cc_start: 0.7589 (t) cc_final: 0.7149 (p) REVERT: A 596 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7320 (ttpp) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.5128 time to fit residues: 54.7852 Evaluate side-chains 95 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1408 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 495 GLN A 545 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105626 restraints weight = 9812.352| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.43 r_work: 0.3258 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7260 Z= 0.205 Angle : 0.667 10.540 10166 Z= 0.370 Chirality : 0.050 0.303 1208 Planarity : 0.005 0.050 1104 Dihedral : 24.931 179.497 1530 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.83 % Allowed : 21.80 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.26 (0.30), residues: 767 helix: 0.49 (0.23), residues: 526 sheet: 2.65 (1.03), residues: 23 loop : -2.05 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 6 TYR 0.014 0.002 TYR D1316 PHE 0.011 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 ( 7257) covalent geometry : angle 0.66689 / 0.37 (10166) hydrogen bonds : bond 0.05090 / 3.52 ( 325) hydrogen bonds : angle 4.36597 / 3.20 ( 963) metal coordination : bond 0.01115 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.242 Fit side-chains REVERT: A 414 GLU cc_start: 0.7973 (mp0) cc_final: 0.7727 (mp0) REVERT: A 576 CYS cc_start: 0.7577 (t) cc_final: 0.7149 (p) REVERT: A 596 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7370 (ttpp) REVERT: D 1381 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7395 (mt-10) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 0.5120 time to fit residues: 55.8458 Evaluate side-chains 104 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1328 VAL Chi-restraints excluded: chain D residue 1408 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 495 GLN A 545 HIS D1378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106004 restraints weight = 9620.683| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.54 r_work: 0.3233 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7260 Z= 0.202 Angle : 0.671 11.689 10166 Z= 0.372 Chirality : 0.050 0.308 1208 Planarity : 0.005 0.052 1104 Dihedral : 24.983 179.473 1530 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.00 % Allowed : 22.30 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.23 (0.30), residues: 767 helix: 0.52 (0.23), residues: 524 sheet: 2.58 (1.05), residues: 23 loop : -2.05 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 6 TYR 0.012 0.001 TYR D1317 PHE 0.011 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 7257) covalent geometry : angle 0.67114 / 0.37 (10166) hydrogen bonds : bond 0.04918 / 3.40 ( 325) hydrogen bonds : angle 4.39061 / 3.23 ( 963) metal coordination : bond 0.01055 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.193 Fit side-chains REVERT: A 86 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: A 414 GLU cc_start: 0.8009 (mp0) cc_final: 0.7792 (mp0) REVERT: A 448 GLU cc_start: 0.7367 (mp0) cc_final: 0.7144 (mp0) REVERT: A 576 CYS cc_start: 0.7663 (t) cc_final: 0.7274 (p) REVERT: A 596 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7425 (ttpp) REVERT: D 1354 MET cc_start: 0.8126 (ttm) cc_final: 0.7916 (ttp) REVERT: D 1381 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7337 (mt-10) outliers start: 18 outliers final: 8 residues processed: 104 average time/residue: 0.5054 time to fit residues: 55.6192 Evaluate side-chains 100 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 495 GLN A 545 HIS D1378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107847 restraints weight = 9653.549| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.55 r_work: 0.3267 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7260 Z= 0.154 Angle : 0.638 9.923 10166 Z= 0.354 Chirality : 0.047 0.302 1208 Planarity : 0.005 0.052 1104 Dihedral : 25.037 179.457 1530 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.00 % Allowed : 23.13 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.09 (0.30), residues: 767 helix: 0.62 (0.23), residues: 522 sheet: 2.52 (1.05), residues: 23 loop : -1.93 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 6 TYR 0.006 0.001 TYR D1317 PHE 0.006 0.001 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.002 0.000 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 7257) covalent geometry : angle 0.63835 / 0.35 (10166) hydrogen bonds : bond 0.03881 / 2.67 ( 325) hydrogen bonds : angle 4.31307 / 3.16 ( 963) metal coordination : bond 0.00492 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.221 Fit side-chains REVERT: A 86 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8015 (mtm110) REVERT: A 414 GLU cc_start: 0.7972 (mp0) cc_final: 0.7761 (mp0) REVERT: A 576 CYS cc_start: 0.7635 (t) cc_final: 0.7242 (p) REVERT: A 596 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7470 (ttpp) REVERT: D 1354 MET cc_start: 0.8098 (ttm) cc_final: 0.7875 (ttp) REVERT: D 1381 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7399 (mt-10) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 0.5616 time to fit residues: 55.1261 Evaluate side-chains 95 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.0670 chunk 20 optimal weight: 0.0980 chunk 27 optimal weight: 0.0070 chunk 29 optimal weight: 0.5980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN A 545 HIS D1378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108986 restraints weight = 9588.600| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.54 r_work: 0.3277 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7260 Z= 0.145 Angle : 0.626 9.379 10166 Z= 0.347 Chirality : 0.045 0.302 1208 Planarity : 0.005 0.052 1104 Dihedral : 25.067 178.997 1530 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.83 % Allowed : 23.63 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.04 (0.30), residues: 767 helix: 0.72 (0.23), residues: 522 sheet: 2.52 (1.07), residues: 23 loop : -1.86 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 6 TYR 0.005 0.001 TYR D1317 PHE 0.006 0.001 PHE D1412 TRP 0.004 0.001 TRP A 82 HIS 0.002 0.000 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 7257) covalent geometry : angle 0.62635 / 0.35 (10166) hydrogen bonds : bond 0.03540 / 2.43 ( 325) hydrogen bonds : angle 4.24373 / 3.11 ( 963) metal coordination : bond 0.00581 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.236 Fit side-chains REVERT: A 86 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7972 (mtm110) REVERT: A 275 LEU cc_start: 0.7950 (mp) cc_final: 0.7695 (mt) REVERT: A 414 GLU cc_start: 0.7980 (mp0) cc_final: 0.7761 (mp0) REVERT: A 576 CYS cc_start: 0.7624 (t) cc_final: 0.7240 (p) REVERT: D 1354 MET cc_start: 0.8051 (ttm) cc_final: 0.7808 (ttp) REVERT: D 1381 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7413 (mt-10) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.5584 time to fit residues: 54.1752 Evaluate side-chains 93 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 1328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN A 545 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107810 restraints weight = 9628.173| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.54 r_work: 0.3268 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7260 Z= 0.168 Angle : 0.645 11.548 10166 Z= 0.356 Chirality : 0.047 0.309 1208 Planarity : 0.005 0.062 1104 Dihedral : 25.062 179.896 1530 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 23.79 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.02 (0.30), residues: 767 helix: 0.69 (0.23), residues: 522 sheet: 2.52 (1.06), residues: 23 loop : -1.83 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 6 TYR 0.009 0.001 TYR D1317 PHE 0.007 0.001 PHE D1375 TRP 0.005 0.001 TRP A 82 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 7257) covalent geometry : angle 0.64521 / 0.36 (10166) hydrogen bonds : bond 0.04103 / 2.83 ( 325) hydrogen bonds : angle 4.27577 / 3.13 ( 963) metal coordination : bond 0.00791 / 0.39 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.239 Fit side-chains REVERT: A 86 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8028 (mtm110) REVERT: A 275 LEU cc_start: 0.7960 (mp) cc_final: 0.7715 (mt) REVERT: A 414 GLU cc_start: 0.8010 (mp0) cc_final: 0.7790 (mp0) REVERT: A 576 CYS cc_start: 0.7625 (t) cc_final: 0.7250 (p) REVERT: D 1354 MET cc_start: 0.8068 (ttm) cc_final: 0.7842 (ttp) REVERT: D 1381 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7414 (mt-10) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.5324 time to fit residues: 52.6070 Evaluate side-chains 97 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain D residue 1328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN A 545 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106535 restraints weight = 9746.864| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.42 r_work: 0.3277 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7260 Z= 0.185 Angle : 0.664 11.374 10166 Z= 0.366 Chirality : 0.048 0.316 1208 Planarity : 0.005 0.052 1104 Dihedral : 25.073 179.975 1530 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.16 % Allowed : 23.79 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.14 (0.30), residues: 767 helix: 0.59 (0.23), residues: 524 sheet: 2.57 (1.06), residues: 23 loop : -1.98 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 6 TYR 0.010 0.001 TYR D1316 PHE 0.008 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 7257) covalent geometry : angle 0.66411 / 0.37 (10166) hydrogen bonds : bond 0.04465 / 3.09 ( 325) hydrogen bonds : angle 4.30924 / 3.17 ( 963) metal coordination : bond 0.00863 / 0.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.16 seconds wall clock time: 38 minutes 19.02 seconds (2299.02 seconds total)