Starting phenix.real_space_refine on Wed Feb 4 00:02:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo8_61646/02_2026/9jo8_61646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo8_61646/02_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_61646/02_2026/9jo8_61646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo8_61646/02_2026/9jo8_61646.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo8_61646/02_2026/9jo8_61646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo8_61646/02_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-2.0-5952/lib/python3.9/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: 1.29, per 1000 atoms: 0.18 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: 0.79 Conformation dependent library (CDL) restraints added in 236.8 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: 0.72 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: 1.40 Time building geometry restraints manager: 0.99 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=" C ASP A 151 " pdb=" N GLY A 152 " ideal model delta sigma weight residual 1.327 1.291 0.037 1.26e-02 6.30e+03 8.54e+00 bond pdb=" CB PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.90e+00 bond pdb=" N GLN A 631 " pdb=" CA GLN A 631 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.76e+00 ... (remaining 7252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 9910 2.10 - 4.21: 187 4.21 - 6.31: 48 6.31 - 8.41: 11 8.41 - 10.52: 10 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 120.20 109.68 10.52 1.50e+00 4.44e-01 4.92e+01 angle pdb=" C3' DT C 3 " pdb=" O3' DT C 3 " pdb=" P DA C 4 " ideal model delta sigma weight residual 120.20 110.46 9.74 1.50e+00 4.44e-01 4.22e+01 angle pdb=" C ASP A 151 " pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 109.90 119.84 -9.94 1.56e+00 4.11e-01 4.06e+01 angle pdb=" C3' DA B 26 " pdb=" O3' DA B 26 " pdb=" P DT B 27 " ideal model delta sigma weight residual 120.20 110.73 9.47 1.50e+00 4.44e-01 3.99e+01 angle pdb=" C3' DA C 2 " pdb=" O3' DA C 2 " pdb=" P DT C 3 " ideal model delta sigma weight residual 120.20 111.16 9.04 1.50e+00 4.44e-01 3.63e+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 - 0.122: 1190 0.122 - 0.245: 3 0.245 - 0.367: 1 0.367 - 0.489: 12 0.489 - 0.612: 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 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.35e+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 2.35 -2.84 -0.49 2.00e-01 2.50e+01 6.00e+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 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.71e+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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.004 0.121 7260 Z= 0.209 Angle : 0.778 10.517 10166 Z= 0.432 Chirality : 0.064 0.612 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 covalent geometry : bond 0.00448 ( 7257) covalent geometry : angle 0.77840 (10166) hydrogen bonds : bond 0.19256 ( 325) hydrogen bonds : angle 6.00404 ( 963) metal coordination : bond 0.00332 ( 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 : 0.173 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: 0.5299 time to fit residues: 48.4945 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 : 0.233 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106919 restraints weight = 9797.345| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.44 r_work: 0.3281 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7260 Z= 0.184 Angle : 0.602 8.129 10166 Z= 0.331 Chirality : 0.041 0.138 1208 Planarity : 0.005 0.056 1104 Dihedral : 24.634 178.807 1530 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.66 % Allowed : 22.13 % Favored : 75.21 % 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: -0.19 (0.30), residues: 767 helix: 0.47 (0.22), residues: 522 sheet: 2.12 (0.96), residues: 25 loop : -1.72 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 6 TYR 0.013 0.001 TYR D1316 PHE 0.014 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7257) covalent geometry : angle 0.60230 (10166) hydrogen bonds : bond 0.04719 ( 325) hydrogen bonds : angle 4.55694 ( 963) metal coordination : bond 0.00857 ( 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 106 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.232 Fit side-chains REVERT: A 414 GLU cc_start: 0.7928 (mp0) cc_final: 0.7696 (mp0) REVERT: A 576 CYS cc_start: 0.7603 (t) cc_final: 0.7110 (p) REVERT: A 596 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7445 (ttpt) REVERT: D 1364 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8538 (t) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.5687 time to fit residues: 57.5270 Evaluate side-chains 105 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 344 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain D residue 1328 VAL 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: 0.0270 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 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 = 0.123167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108883 restraints weight = 9716.819| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.43 r_work: 0.3310 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7260 Z= 0.145 Angle : 0.567 8.687 10166 Z= 0.309 Chirality : 0.039 0.193 1208 Planarity : 0.005 0.050 1104 Dihedral : 24.666 177.776 1530 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.66 % Allowed : 21.13 % Favored : 76.21 % 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: 0.61 (0.23), residues: 521 sheet: 2.22 (0.99), residues: 25 loop : -1.60 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 6 TYR 0.008 0.001 TYR D1316 PHE 0.010 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 covalent geometry : bond 0.00324 ( 7257) covalent geometry : angle 0.56688 (10166) hydrogen bonds : bond 0.03681 ( 325) hydrogen bonds : angle 4.32205 ( 963) metal coordination : bond 0.00480 ( 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 98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.227 Fit side-chains REVERT: A 346 GLU cc_start: 0.7187 (mp0) cc_final: 0.6896 (mp0) REVERT: A 414 GLU cc_start: 0.7940 (mp0) cc_final: 0.7717 (mp0) REVERT: A 570 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7999 (ttp80) REVERT: A 576 CYS cc_start: 0.7573 (t) cc_final: 0.7124 (p) REVERT: A 596 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7303 (ttpp) REVERT: A 600 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6935 (mt-10) REVERT: D 1364 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8552 (t) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.6353 time to fit residues: 58.6516 Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 343 LEU Chi-restraints excluded: chain A residue 513 LEU 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: 1.9990 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106717 restraints weight = 9766.483| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.41 r_work: 0.3276 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7260 Z= 0.186 Angle : 0.604 9.080 10166 Z= 0.332 Chirality : 0.041 0.199 1208 Planarity : 0.005 0.050 1104 Dihedral : 24.787 178.815 1530 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 21.96 % 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: -0.12 (0.30), residues: 767 helix: 0.53 (0.23), residues: 525 sheet: 2.21 (0.99), residues: 25 loop : -1.78 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 6 TYR 0.013 0.001 TYR D1316 PHE 0.013 0.002 PHE D1375 TRP 0.003 0.001 TRP A 82 HIS 0.002 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7257) covalent geometry : angle 0.60381 (10166) hydrogen bonds : bond 0.04580 ( 325) hydrogen bonds : angle 4.31754 ( 963) metal coordination : bond 0.00856 ( 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: 19 poor density : 87 time to evaluate : 0.234 Fit side-chains REVERT: A 414 GLU cc_start: 0.7969 (mp0) cc_final: 0.7721 (mp0) REVERT: A 576 CYS cc_start: 0.7531 (t) cc_final: 0.7104 (p) REVERT: A 596 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7404 (ttpp) REVERT: D 1364 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8587 (t) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.5676 time to fit residues: 56.7727 Evaluate side-chains 95 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR 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 344 THR Chi-restraints excluded: chain A residue 368 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 29 optimal weight: 0.1980 chunk 36 optimal weight: 0.3980 chunk 73 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107394 restraints weight = 9876.548| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.44 r_work: 0.3288 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7260 Z= 0.165 Angle : 0.589 9.621 10166 Z= 0.323 Chirality : 0.040 0.188 1208 Planarity : 0.005 0.051 1104 Dihedral : 24.784 178.408 1530 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.66 % Allowed : 22.30 % 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: -0.01 (0.30), residues: 767 helix: 0.65 (0.23), residues: 522 sheet: 2.57 (1.02), residues: 23 loop : -1.81 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 6 TYR 0.009 0.001 TYR D1316 PHE 0.010 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.002 0.000 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7257) covalent geometry : angle 0.58880 (10166) hydrogen bonds : bond 0.03948 ( 325) hydrogen bonds : angle 4.25247 ( 963) metal coordination : bond 0.00667 ( 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 98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.237 Fit side-chains REVERT: A 86 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7924 (mtm110) REVERT: A 229 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: A 275 LEU cc_start: 0.7731 (mp) cc_final: 0.7488 (mt) REVERT: A 414 GLU cc_start: 0.7986 (mp0) cc_final: 0.7736 (mp0) REVERT: A 571 LEU cc_start: 0.8024 (mt) cc_final: 0.7723 (mp) REVERT: A 576 CYS cc_start: 0.7518 (t) cc_final: 0.7094 (p) REVERT: A 596 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7292 (ttpt) REVERT: D 1354 MET cc_start: 0.7945 (ttm) cc_final: 0.7708 (ttm) REVERT: D 1364 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8580 (t) REVERT: D 1381 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7328 (mt-10) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.5981 time to fit residues: 56.0452 Evaluate side-chains 94 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 229 GLN 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 596 LYS Chi-restraints excluded: chain D residue 1328 VAL Chi-restraints excluded: chain D residue 1364 VAL 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: 0.0770 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105875 restraints weight = 9849.128| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.44 r_work: 0.3264 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7260 Z= 0.192 Angle : 0.619 9.447 10166 Z= 0.341 Chirality : 0.042 0.188 1208 Planarity : 0.005 0.051 1104 Dihedral : 24.849 178.315 1530 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.49 % Allowed : 21.96 % 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: -0.12 (0.30), residues: 767 helix: 0.61 (0.23), residues: 525 sheet: 2.34 (1.02), residues: 23 loop : -1.97 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 6 TYR 0.010 0.001 TYR D1316 PHE 0.011 0.002 PHE D1375 TRP 0.003 0.001 TRP A 82 HIS 0.002 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 7257) covalent geometry : angle 0.61856 (10166) hydrogen bonds : bond 0.04504 ( 325) hydrogen bonds : angle 4.31924 ( 963) metal coordination : bond 0.00824 ( 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 107 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.190 Fit side-chains REVERT: A 86 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7983 (mtm110) REVERT: A 229 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: A 275 LEU cc_start: 0.7828 (mp) cc_final: 0.7578 (mt) REVERT: A 414 GLU cc_start: 0.7996 (mp0) cc_final: 0.7744 (mp0) REVERT: A 571 LEU cc_start: 0.8031 (mt) cc_final: 0.7745 (mp) REVERT: D 1354 MET cc_start: 0.7952 (ttm) cc_final: 0.7748 (ttp) REVERT: D 1364 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8599 (t) REVERT: D 1381 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7320 (mt-10) outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 0.5079 time to fit residues: 51.9229 Evaluate side-chains 97 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 229 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 609 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105043 restraints weight = 9849.722| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.43 r_work: 0.3252 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7260 Z= 0.215 Angle : 0.646 12.908 10166 Z= 0.354 Chirality : 0.043 0.193 1208 Planarity : 0.005 0.052 1104 Dihedral : 24.845 178.982 1530 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.83 % Allowed : 22.63 % 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: -0.20 (0.30), residues: 767 helix: 0.56 (0.23), residues: 525 sheet: 2.27 (1.02), residues: 23 loop : -2.03 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 99 TYR 0.012 0.001 TYR D1316 PHE 0.011 0.002 PHE D1375 TRP 0.004 0.001 TRP A 82 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 7257) covalent geometry : angle 0.64571 (10166) hydrogen bonds : bond 0.04789 ( 325) hydrogen bonds : angle 4.35266 ( 963) metal coordination : bond 0.01032 ( 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 102 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.141 Fit side-chains REVERT: A 86 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8000 (mtm110) REVERT: A 229 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: A 275 LEU cc_start: 0.7844 (mp) cc_final: 0.7621 (mt) REVERT: A 414 GLU cc_start: 0.8009 (mp0) cc_final: 0.7764 (mp0) REVERT: A 571 LEU cc_start: 0.8027 (mt) cc_final: 0.7760 (mp) REVERT: A 576 CYS cc_start: 0.7556 (t) cc_final: 0.7141 (p) REVERT: D 1364 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8608 (t) REVERT: D 1381 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7330 (mt-10) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.5265 time to fit residues: 51.5466 Evaluate side-chains 97 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 GLN 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 606 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain D residue 1328 VAL Chi-restraints excluded: chain D residue 1364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.3980 chunk 35 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108851 restraints weight = 9869.278| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.44 r_work: 0.3313 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7260 Z= 0.146 Angle : 0.598 12.140 10166 Z= 0.323 Chirality : 0.039 0.183 1208 Planarity : 0.005 0.053 1104 Dihedral : 24.713 178.741 1530 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.33 % Allowed : 23.96 % Favored : 73.71 % 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: 0.08 (0.30), residues: 767 helix: 0.74 (0.23), residues: 520 sheet: 2.09 (1.04), residues: 25 loop : -1.78 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 570 TYR 0.007 0.001 TYR D1316 PHE 0.008 0.001 PHE D1375 TRP 0.004 0.001 TRP A 128 HIS 0.003 0.000 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7257) covalent geometry : angle 0.59794 (10166) hydrogen bonds : bond 0.03199 ( 325) hydrogen bonds : angle 4.16488 ( 963) metal coordination : bond 0.00462 ( 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 102 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.237 Fit side-chains REVERT: A 86 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7855 (mtm110) REVERT: A 275 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 354 ASN cc_start: 0.7269 (m-40) cc_final: 0.7054 (m-40) REVERT: A 414 GLU cc_start: 0.7964 (mp0) cc_final: 0.7731 (mp0) REVERT: A 571 LEU cc_start: 0.7991 (mt) cc_final: 0.7723 (mp) REVERT: A 576 CYS cc_start: 0.7512 (t) cc_final: 0.7101 (p) REVERT: D 1364 VAL cc_start: 0.8773 (t) cc_final: 0.8558 (t) REVERT: D 1381 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7333 (mt-10) outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 0.5705 time to fit residues: 57.7002 Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 609 LEU 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: 0.6980 chunk 78 optimal weight: 0.0770 chunk 7 optimal weight: 0.0570 chunk 74 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110059 restraints weight = 9793.403| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.44 r_work: 0.3327 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7260 Z= 0.135 Angle : 0.569 11.798 10166 Z= 0.307 Chirality : 0.038 0.127 1208 Planarity : 0.005 0.052 1104 Dihedral : 24.684 178.637 1530 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.66 % Allowed : 24.96 % Favored : 73.38 % 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: 0.14 (0.30), residues: 767 helix: 0.77 (0.23), residues: 522 sheet: 2.18 (1.08), residues: 25 loop : -1.73 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 570 TYR 0.006 0.001 TYR D1316 PHE 0.007 0.001 PHE D1375 TRP 0.005 0.001 TRP A 82 HIS 0.002 0.000 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7257) covalent geometry : angle 0.56922 (10166) hydrogen bonds : bond 0.03065 ( 325) hydrogen bonds : angle 4.11370 ( 963) metal coordination : bond 0.00352 ( 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 95 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.257 Fit side-chains REVERT: A 86 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7856 (mtm110) REVERT: A 275 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7601 (mt) REVERT: A 414 GLU cc_start: 0.7955 (mp0) cc_final: 0.7711 (mp0) REVERT: A 571 LEU cc_start: 0.7960 (mt) cc_final: 0.7704 (mp) REVERT: D 1364 VAL cc_start: 0.8757 (t) cc_final: 0.8537 (t) REVERT: D 1381 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7325 (mt-10) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.5203 time to fit residues: 49.9825 Evaluate side-chains 92 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 VAL 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 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108325 restraints weight = 9808.301| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.44 r_work: 0.3297 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1871 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= 0.159 Angle : 0.607 11.623 10166 Z= 0.328 Chirality : 0.040 0.122 1208 Planarity : 0.005 0.052 1104 Dihedral : 24.672 179.062 1530 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.33 % Allowed : 25.96 % Favored : 72.71 % 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: 0.12 (0.30), residues: 767 helix: 0.75 (0.23), residues: 522 sheet: 2.15 (1.07), residues: 25 loop : -1.73 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 570 TYR 0.008 0.001 TYR D1316 PHE 0.010 0.001 PHE D1375 TRP 0.005 0.001 TRP A 82 HIS 0.002 0.000 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7257) covalent geometry : angle 0.60712 (10166) hydrogen bonds : bond 0.03629 ( 325) hydrogen bonds : angle 4.16162 ( 963) metal coordination : bond 0.00576 ( 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 86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.248 Fit side-chains REVERT: A 86 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (mtm110) REVERT: A 275 LEU cc_start: 0.7840 (mp) cc_final: 0.7627 (mt) REVERT: A 414 GLU cc_start: 0.7999 (mp0) cc_final: 0.7753 (mp0) REVERT: A 571 LEU cc_start: 0.8007 (mt) cc_final: 0.7733 (mp) REVERT: A 576 CYS cc_start: 0.7516 (t) cc_final: 0.7139 (p) REVERT: D 1364 VAL cc_start: 0.8801 (t) cc_final: 0.8591 (t) REVERT: D 1381 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7309 (mt-10) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.6001 time to fit residues: 52.4710 Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG 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 513 LEU Chi-restraints excluded: chain A residue 540 VAL 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: 0.0770 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107247 restraints weight = 9742.253| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.43 r_work: 0.3279 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7260 Z= 0.169 Angle : 0.614 11.431 10166 Z= 0.333 Chirality : 0.040 0.121 1208 Planarity : 0.005 0.052 1104 Dihedral : 24.667 178.251 1530 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.66 % Allowed : 25.62 % Favored : 72.71 % 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: 0.09 (0.30), residues: 767 helix: 0.74 (0.23), residues: 521 sheet: 2.42 (1.08), residues: 23 loop : -1.76 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 570 TYR 0.009 0.001 TYR D1316 PHE 0.010 0.001 PHE D1375 TRP 0.005 0.001 TRP A 82 HIS 0.002 0.000 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7257) covalent geometry : angle 0.61408 (10166) hydrogen bonds : bond 0.03943 ( 325) hydrogen bonds : angle 4.20454 ( 963) metal coordination : bond 0.00624 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.10 seconds wall clock time: 38 minutes 36.96 seconds (2316.96 seconds total)