Starting phenix.real_space_refine on Fri Jul 3 01:39:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.map" model { file = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2026/7eld_31181.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 109 5.49 5 S 60 5.16 5 C 6758 2.51 5 N 1946 2.21 5 O 2409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11282 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8976 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 38, 'TRANS': 1098} Chain breaks: 12 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2306 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 48, 'rna3p_pyr': 56} Link IDs: {'rna2p': 4, 'rna3p': 104} Chain breaks: 6 Time building chain proxies: 2.23, per 1000 atoms: 0.20 Number of scatterers: 11282 At special positions: 0 Unit cell: (95.316, 110.526, 188.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 109 15.00 O 2409 8.00 N 1946 7.00 C 6758 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: 0.80 Conformation dependent library (CDL) restraints added in 463.0 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 57.7% alpha, 4.7% beta 43 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.523A pdb=" N ASP A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 removed outlier: 4.099A pdb=" N MET A 297 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.847A pdb=" N ASN A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 348 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.980A pdb=" N ILE A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.655A pdb=" N LEU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 472 through 493 removed outlier: 3.685A pdb=" N THR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 567 removed outlier: 6.980A pdb=" N GLN A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N TRP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 594 removed outlier: 4.276A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.856A pdb=" N HIS A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 673 through 687 Proline residue: A 681 - end of helix removed outlier: 3.650A pdb=" N LEU A 687 " --> pdb=" O VAL A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 721 removed outlier: 3.592A pdb=" N ASP A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 781 through 800 removed outlier: 3.905A pdb=" N PHE A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 827 through 851 removed outlier: 4.079A pdb=" N THR A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 920 Processing helix chain 'A' and resid 1049 through 1064 Processing helix chain 'A' and resid 1064 through 1069 Processing helix chain 'A' and resid 1103 through 1113 Processing helix chain 'A' and resid 1254 through 1264 Processing helix chain 'A' and resid 1301 through 1307 removed outlier: 3.580A pdb=" N VAL A1307 " --> pdb=" O LYS A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1348 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1356 through 1364 Processing helix chain 'A' and resid 1374 through 1397 Processing helix chain 'A' and resid 1401 through 1414 Processing helix chain 'A' and resid 1414 through 1426 Processing helix chain 'A' and resid 1501 through 1517 Processing helix chain 'A' and resid 1518 through 1529 Processing helix chain 'A' and resid 1559 through 1567 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.707A pdb=" N LEU A1576 " --> pdb=" O GLU A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1615 removed outlier: 4.443A pdb=" N LEU A1596 " --> pdb=" O CYS A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1632 Processing helix chain 'A' and resid 1633 through 1644 Processing helix chain 'A' and resid 1645 through 1650 Processing helix chain 'A' and resid 1654 through 1668 Processing helix chain 'A' and resid 1690 through 1706 Processing helix chain 'A' and resid 1709 through 1726 removed outlier: 3.524A pdb=" N ALA A1713 " --> pdb=" O ASP A1709 " (cutoff:3.500A) Proline residue: A1719 - end of helix Proline residue: A1723 - end of helix removed outlier: 3.913A pdb=" N THR A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1742 Processing helix chain 'A' and resid 1780 through 1794 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.623A pdb=" N GLY A 325 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 301 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 300 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 464 removed outlier: 5.453A pdb=" N ILE A 461 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 775 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 463 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 862 through 867 Processing sheet with id=AA5, first strand: chain 'A' and resid 1036 through 1041 removed outlier: 4.343A pdb=" N PHE A1009 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A1086 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1211 through 1212 Processing sheet with id=AA7, first strand: chain 'A' and resid 1230 through 1231 Processing sheet with id=AA8, first strand: chain 'A' and resid 1760 through 1761 removed outlier: 3.683A pdb=" N ALA A1760 " --> pdb=" O GLY A1772 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1883 1.32 - 1.45: 3390 1.45 - 1.57: 6121 1.57 - 1.69: 211 1.69 - 1.81: 96 Bond restraints: 11701 Sorted by residual: bond pdb=" C VAL A 828 " pdb=" O VAL A 828 " ideal model delta sigma weight residual 1.237 1.321 -0.084 1.19e-02 7.06e+03 4.97e+01 bond pdb=" C VAL A 841 " pdb=" O VAL A 841 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.13e-02 7.83e+03 3.74e+01 bond pdb=" C ASN A 838 " pdb=" O ASN A 838 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.17e-02 7.31e+03 3.03e+01 bond pdb=" C TYR A 847 " pdb=" O TYR A 847 " ideal model delta sigma weight residual 1.237 1.298 -0.062 1.17e-02 7.31e+03 2.77e+01 bond pdb=" N VAL A 303 " pdb=" CA VAL A 303 " ideal model delta sigma weight residual 1.454 1.494 -0.040 7.70e-03 1.69e+04 2.69e+01 ... (remaining 11696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13871 2.21 - 4.43: 2358 4.43 - 6.64: 60 6.64 - 8.85: 9 8.85 - 11.07: 2 Bond angle restraints: 16300 Sorted by residual: angle pdb=" O3' U B 115 " pdb=" C3' U B 115 " pdb=" C2' U B 115 " ideal model delta sigma weight residual 109.50 120.57 -11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" CA LYS A 827 " pdb=" C LYS A 827 " pdb=" N VAL A 828 " ideal model delta sigma weight residual 115.27 123.61 -8.34 1.34e+00 5.57e-01 3.87e+01 angle pdb=" O LYS A 827 " pdb=" C LYS A 827 " pdb=" N VAL A 828 " ideal model delta sigma weight residual 122.79 116.30 6.49 1.14e+00 7.69e-01 3.24e+01 angle pdb=" C ALA A 840 " pdb=" N VAL A 841 " pdb=" CA VAL A 841 " ideal model delta sigma weight residual 120.56 113.45 7.11 1.26e+00 6.30e-01 3.19e+01 angle pdb=" C HIS A 874 " pdb=" N THR A 875 " pdb=" CA THR A 875 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 ... (remaining 16295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 6537 35.28 - 70.55: 303 70.55 - 105.83: 20 105.83 - 141.10: 2 141.10 - 176.38: 1 Dihedral angle restraints: 6863 sinusoidal: 3537 harmonic: 3326 Sorted by residual: dihedral pdb=" C5' U B 115 " pdb=" C4' U B 115 " pdb=" C3' U B 115 " pdb=" O3' U B 115 " ideal model delta sinusoidal sigma weight residual 147.00 89.74 57.26 1 8.00e+00 1.56e-02 6.89e+01 dihedral pdb=" C LEU A 851 " pdb=" N LEU A 851 " pdb=" CA LEU A 851 " pdb=" CB LEU A 851 " ideal model delta harmonic sigma weight residual -122.60 -138.27 15.67 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" O4' C B 27 " pdb=" C1' C B 27 " pdb=" N1 C B 27 " pdb=" C2 C B 27 " ideal model delta sinusoidal sigma weight residual -160.00 -77.36 -82.64 1 1.50e+01 4.44e-03 3.72e+01 ... (remaining 6860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1370 0.122 - 0.245: 576 0.245 - 0.367: 11 0.367 - 0.489: 2 0.489 - 0.611: 2 Chirality restraints: 1961 Sorted by residual: chirality pdb=" C3' U B 115 " pdb=" C4' U B 115 " pdb=" O3' U B 115 " pdb=" C2' U B 115 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA LEU A 851 " pdb=" N LEU A 851 " pdb=" C LEU A 851 " pdb=" CB LEU A 851 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA ASN A1636 " pdb=" N ASN A1636 " pdb=" C ASN A1636 " pdb=" CB ASN A1636 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1958 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 827 " 0.025 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C LYS A 827 " -0.083 2.00e-02 2.50e+03 pdb=" O LYS A 827 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL A 828 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 848 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C CYS A 848 " 0.061 2.00e-02 2.50e+03 pdb=" O CYS A 848 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A 849 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 841 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C VAL A 841 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL A 841 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 842 " -0.021 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4515 2.94 - 3.43: 11264 3.43 - 3.92: 21762 3.92 - 4.41: 24346 4.41 - 4.90: 33229 Nonbonded interactions: 95116 Sorted by model distance: nonbonded pdb=" O HIS A 874 " pdb=" O THR A 875 " model vdw 2.446 3.040 nonbonded pdb=" O5' G B -13 " pdb=" O4' G B -13 " model vdw 2.484 2.432 nonbonded pdb=" O GLU A 799 " pdb=" N ILE A 801 " model vdw 2.495 3.120 nonbonded pdb=" O5' A B -10 " pdb=" O4' A B -10 " model vdw 2.498 2.432 nonbonded pdb=" O5' C B 79 " pdb=" O4' C B 79 " model vdw 2.508 2.432 ... (remaining 95111 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 group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 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 : 0.012 0.084 11701 Z= 0.900 Angle : 1.409 11.065 16300 Z= 1.103 Chirality : 0.108 0.611 1961 Planarity : 0.005 0.059 1664 Dihedral : 17.542 176.377 4703 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.90 % Allowed : 2.88 % Favored : 96.22 % Rotamer: Outliers : 10.68 % Allowed : 12.31 % Favored : 77.01 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.24), residues: 1111 helix: 4.32 (0.18), residues: 605 sheet: 0.85 (0.57), residues: 83 loop : -0.80 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1062 TYR 0.011 0.002 TYR A 757 PHE 0.010 0.001 PHE A1613 TRP 0.009 0.001 TRP A 547 HIS 0.009 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.90 (11701) covalent geometry : angle 1.40940 / 1.10 (16300) hydrogen bonds : bond 0.16830 / 10.79 ( 570) hydrogen bonds : angle 8.10693 / 5.90 ( 1574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 132 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7906 (p90) REVERT: A 412 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (t) REVERT: A 434 LEU cc_start: 0.9705 (tp) cc_final: 0.9439 (mm) REVERT: A 474 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 552 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8801 (m) REVERT: A 556 PHE cc_start: 0.9188 (m-10) cc_final: 0.8982 (m-80) REVERT: A 794 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9125 (pt0) REVERT: A 803 ARG cc_start: 0.9618 (mtp85) cc_final: 0.9362 (mmp-170) REVERT: A 883 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (mm) REVERT: A 976 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 1200 MET cc_start: 0.7283 (ttm) cc_final: 0.7065 (ttm) REVERT: A 1371 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7104 (p) REVERT: A 1416 MET cc_start: 0.8760 (mmt) cc_final: 0.8411 (mmm) REVERT: A 1497 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8946 (pt) outliers start: 105 outliers final: 25 residues processed: 222 average time/residue: 0.1059 time to fit residues: 32.9786 Evaluate side-chains 116 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 319 GLN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A1328 GLN A1420 GLN A1739 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.046068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.035276 restraints weight = 174220.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.035928 restraints weight = 136108.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.036365 restraints weight = 112981.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.036728 restraints weight = 98756.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.036963 restraints weight = 88750.259| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11701 Z= 0.202 Angle : 0.741 9.285 16300 Z= 0.393 Chirality : 0.042 0.219 1961 Planarity : 0.005 0.056 1664 Dihedral : 16.725 170.952 2513 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.61 % Favored : 96.94 % Rotamer: Outliers : 0.41 % Allowed : 3.46 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1111 helix: 2.04 (0.19), residues: 623 sheet: -0.10 (0.59), residues: 67 loop : -1.06 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 317 TYR 0.027 0.002 TYR A1513 PHE 0.026 0.003 PHE A 846 TRP 0.025 0.003 TRP A1528 HIS 0.014 0.002 HIS A1401 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (11701) covalent geometry : angle 0.74055 / 0.39 (16300) hydrogen bonds : bond 0.06253 / 4.31 ( 570) hydrogen bonds : angle 4.96344 / 3.58 ( 1574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9322 (mm) cc_final: 0.9064 (pp) REVERT: A 707 MET cc_start: 0.1629 (tpt) cc_final: 0.0906 (tpp) REVERT: A 712 MET cc_start: 0.9617 (ttm) cc_final: 0.9265 (mtp) REVERT: A 865 MET cc_start: 0.7505 (pmm) cc_final: 0.6712 (tpp) REVERT: A 1408 MET cc_start: 0.9766 (mtm) cc_final: 0.9462 (mtp) REVERT: A 1416 MET cc_start: 0.8763 (mmt) cc_final: 0.8240 (mmm) REVERT: A 1696 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8841 (mt-10) outliers start: 4 outliers final: 1 residues processed: 93 average time/residue: 0.1120 time to fit residues: 14.5216 Evaluate side-chains 65 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 8.9990 chunk 75 optimal weight: 40.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS A 433 ASN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 HIS A1582 HIS ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.044491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.033842 restraints weight = 177377.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.034442 restraints weight = 138839.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.034888 restraints weight = 116052.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.035197 restraints weight = 101294.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.035360 restraints weight = 91603.725| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11701 Z= 0.155 Angle : 0.661 9.724 16300 Z= 0.346 Chirality : 0.039 0.206 1961 Planarity : 0.005 0.101 1664 Dihedral : 16.681 171.698 2513 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.33 % Favored : 96.31 % Rotamer: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1111 helix: 1.65 (0.20), residues: 619 sheet: -0.46 (0.52), residues: 91 loop : -1.09 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.013 0.002 TYR A 757 PHE 0.022 0.002 PHE A 785 TRP 0.019 0.002 TRP A1528 HIS 0.004 0.001 HIS A 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (11701) covalent geometry : angle 0.66066 / 0.35 (16300) hydrogen bonds : bond 0.05867 / 4.12 ( 570) hydrogen bonds : angle 4.79074 / 3.46 ( 1574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.4296 (mtp) cc_final: 0.3975 (mtp) REVERT: A 474 LEU cc_start: 0.9379 (mm) cc_final: 0.9101 (pp) REVERT: A 712 MET cc_start: 0.9575 (ttm) cc_final: 0.9293 (mtp) REVERT: A 773 LEU cc_start: 0.9245 (mt) cc_final: 0.9034 (mt) REVERT: A 865 MET cc_start: 0.7606 (pmm) cc_final: 0.6621 (tpp) REVERT: A 1026 MET cc_start: 0.8883 (mpp) cc_final: 0.8607 (mpp) REVERT: A 1408 MET cc_start: 0.9749 (mtm) cc_final: 0.9328 (ptp) REVERT: A 1416 MET cc_start: 0.8785 (mmt) cc_final: 0.8272 (mmm) REVERT: A 1597 GLU cc_start: 0.9096 (pt0) cc_final: 0.8819 (pt0) REVERT: A 1637 PHE cc_start: 0.9652 (m-10) cc_final: 0.9396 (m-10) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0933 time to fit residues: 11.3021 Evaluate side-chains 64 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.043065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.032693 restraints weight = 181267.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.033228 restraints weight = 143983.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.033618 restraints weight = 121879.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.033914 restraints weight = 107729.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.034140 restraints weight = 98096.867| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11701 Z= 0.163 Angle : 0.649 8.181 16300 Z= 0.342 Chirality : 0.039 0.214 1961 Planarity : 0.005 0.097 1664 Dihedral : 16.594 172.067 2513 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.78 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1111 helix: 1.60 (0.20), residues: 613 sheet: -0.62 (0.51), residues: 93 loop : -1.31 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 694 TYR 0.013 0.002 TYR A1514 PHE 0.038 0.002 PHE A1372 TRP 0.020 0.002 TRP A1528 HIS 0.013 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (11701) covalent geometry : angle 0.64919 / 0.34 (16300) hydrogen bonds : bond 0.06149 / 4.34 ( 570) hydrogen bonds : angle 4.80805 / 3.48 ( 1574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9307 (mm) cc_final: 0.9000 (pp) REVERT: A 712 MET cc_start: 0.9561 (ttm) cc_final: 0.9331 (mpp) REVERT: A 773 LEU cc_start: 0.9173 (mt) cc_final: 0.8949 (mt) REVERT: A 847 TYR cc_start: 0.8811 (t80) cc_final: 0.8497 (t80) REVERT: A 865 MET cc_start: 0.7544 (pmm) cc_final: 0.6569 (tpp) REVERT: A 1026 MET cc_start: 0.8904 (mpp) cc_final: 0.8642 (mpp) REVERT: A 1201 MET cc_start: 0.8368 (tpt) cc_final: 0.8112 (tpp) REVERT: A 1385 LEU cc_start: 0.9632 (tp) cc_final: 0.9410 (mm) REVERT: A 1408 MET cc_start: 0.9690 (mtm) cc_final: 0.9421 (mtp) REVERT: A 1416 MET cc_start: 0.8775 (mmt) cc_final: 0.8237 (mmm) REVERT: A 1597 GLU cc_start: 0.9093 (pt0) cc_final: 0.8781 (pt0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0897 time to fit residues: 9.8883 Evaluate side-chains 60 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 73 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1328 GLN A1744 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.042338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032118 restraints weight = 181078.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.032641 restraints weight = 145234.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.033026 restraints weight = 123162.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.033241 restraints weight = 109175.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.033499 restraints weight = 100650.575| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11701 Z= 0.153 Angle : 0.639 9.027 16300 Z= 0.334 Chirality : 0.039 0.272 1961 Planarity : 0.005 0.092 1664 Dihedral : 16.406 172.689 2513 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.23 % Favored : 95.41 % Rotamer: Outliers : 0.20 % Allowed : 3.05 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1111 helix: 1.49 (0.20), residues: 613 sheet: -0.81 (0.51), residues: 93 loop : -1.39 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.016 0.002 TYR A1255 PHE 0.022 0.002 PHE A 846 TRP 0.020 0.002 TRP A1528 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (11701) covalent geometry : angle 0.63851 / 0.33 (16300) hydrogen bonds : bond 0.05764 / 4.05 ( 570) hydrogen bonds : angle 4.84145 / 3.52 ( 1574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9296 (mm) cc_final: 0.8952 (pp) REVERT: A 712 MET cc_start: 0.9574 (ttm) cc_final: 0.9306 (mpp) REVERT: A 865 MET cc_start: 0.7505 (pmm) cc_final: 0.6476 (mmm) REVERT: A 1026 MET cc_start: 0.8761 (mpp) cc_final: 0.8548 (mpp) REVERT: A 1385 LEU cc_start: 0.9646 (tp) cc_final: 0.9413 (mm) REVERT: A 1408 MET cc_start: 0.9749 (mtm) cc_final: 0.9406 (mtp) REVERT: A 1416 MET cc_start: 0.8860 (mmt) cc_final: 0.8318 (mmm) REVERT: A 1597 GLU cc_start: 0.9071 (pt0) cc_final: 0.8839 (pt0) REVERT: A 1744 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8131 (mp10) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.0837 time to fit residues: 9.8705 Evaluate side-chains 61 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 398 HIS ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN A1606 HIS ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.040564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.030642 restraints weight = 188940.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.031154 restraints weight = 150231.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.031538 restraints weight = 126682.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.031811 restraints weight = 111627.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.031961 restraints weight = 101725.534| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11701 Z= 0.197 Angle : 0.700 8.260 16300 Z= 0.368 Chirality : 0.040 0.244 1961 Planarity : 0.005 0.095 1664 Dihedral : 16.589 172.587 2513 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.22 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1111 helix: 1.32 (0.21), residues: 613 sheet: -1.02 (0.52), residues: 93 loop : -1.55 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 405 TYR 0.015 0.002 TYR A 327 PHE 0.041 0.003 PHE A1372 TRP 0.022 0.003 TRP A1528 HIS 0.008 0.002 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (11701) covalent geometry : angle 0.69966 / 0.37 (16300) hydrogen bonds : bond 0.06808 / 4.75 ( 570) hydrogen bonds : angle 5.05516 / 3.67 ( 1574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.6771 (mmm) cc_final: 0.6435 (mpp) REVERT: A 369 MET cc_start: 0.4265 (mtp) cc_final: 0.3783 (mtp) REVERT: A 548 CYS cc_start: 0.9317 (t) cc_final: 0.8297 (p) REVERT: A 680 LEU cc_start: 0.9620 (tp) cc_final: 0.9379 (tp) REVERT: A 712 MET cc_start: 0.9598 (ttm) cc_final: 0.9370 (mpp) REVERT: A 865 MET cc_start: 0.7629 (pmm) cc_final: 0.6671 (tpt) REVERT: A 1026 MET cc_start: 0.8827 (mpp) cc_final: 0.8562 (mpp) REVERT: A 1385 LEU cc_start: 0.9682 (tp) cc_final: 0.9455 (mm) REVERT: A 1408 MET cc_start: 0.9710 (mtm) cc_final: 0.9446 (mtp) REVERT: A 1416 MET cc_start: 0.8805 (mmt) cc_final: 0.8296 (mmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0831 time to fit residues: 8.9235 Evaluate side-chains 59 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 48 optimal weight: 40.0000 chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 40.0000 chunk 82 optimal weight: 0.2980 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 40.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1718 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.041340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.031178 restraints weight = 184549.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.031705 restraints weight = 145907.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.032098 restraints weight = 123108.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.032388 restraints weight = 108265.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.032598 restraints weight = 98409.569| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11701 Z= 0.148 Angle : 0.644 9.226 16300 Z= 0.334 Chirality : 0.039 0.238 1961 Planarity : 0.005 0.087 1664 Dihedral : 16.300 173.313 2513 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.59 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1111 helix: 1.38 (0.21), residues: 618 sheet: -1.10 (0.52), residues: 93 loop : -1.60 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 317 TYR 0.012 0.001 TYR A1649 PHE 0.025 0.002 PHE A1372 TRP 0.020 0.002 TRP A1528 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (11701) covalent geometry : angle 0.64388 / 0.33 (16300) hydrogen bonds : bond 0.05444 / 3.76 ( 570) hydrogen bonds : angle 4.96006 / 3.59 ( 1574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 CYS cc_start: 0.9393 (t) cc_final: 0.8337 (p) REVERT: A 712 MET cc_start: 0.9638 (ttm) cc_final: 0.9386 (mpp) REVERT: A 746 MET cc_start: 0.9235 (tmm) cc_final: 0.9022 (tmm) REVERT: A 865 MET cc_start: 0.7570 (pmm) cc_final: 0.6598 (tpt) REVERT: A 1026 MET cc_start: 0.8924 (mpp) cc_final: 0.8603 (mpp) REVERT: A 1385 LEU cc_start: 0.9644 (tp) cc_final: 0.9413 (mm) REVERT: A 1408 MET cc_start: 0.9759 (mtm) cc_final: 0.9489 (mtp) REVERT: A 1412 MET cc_start: 0.8247 (mtm) cc_final: 0.8013 (mtm) REVERT: A 1416 MET cc_start: 0.8841 (mmt) cc_final: 0.8320 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0880 time to fit residues: 9.3482 Evaluate side-chains 57 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 112 optimal weight: 40.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.040083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.030097 restraints weight = 189177.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.030614 restraints weight = 149469.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.031001 restraints weight = 125633.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.031263 restraints weight = 110371.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.031473 restraints weight = 100690.422| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11701 Z= 0.189 Angle : 0.690 8.546 16300 Z= 0.361 Chirality : 0.040 0.224 1961 Planarity : 0.005 0.092 1664 Dihedral : 16.502 172.881 2513 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.22 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1111 helix: 1.10 (0.21), residues: 619 sheet: -1.12 (0.55), residues: 89 loop : -1.76 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.016 0.002 TYR A 327 PHE 0.023 0.003 PHE A 785 TRP 0.031 0.003 TRP A1528 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (11701) covalent geometry : angle 0.68980 / 0.36 (16300) hydrogen bonds : bond 0.06614 / 4.61 ( 570) hydrogen bonds : angle 5.14935 / 3.70 ( 1574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7992 (mmm) cc_final: 0.7273 (mpp) REVERT: A 353 MET cc_start: 0.9328 (pmm) cc_final: 0.9063 (pmm) REVERT: A 712 MET cc_start: 0.9698 (ttm) cc_final: 0.9441 (mpp) REVERT: A 865 MET cc_start: 0.7594 (pmm) cc_final: 0.6490 (tpt) REVERT: A 1026 MET cc_start: 0.8642 (mpp) cc_final: 0.8310 (mpp) REVERT: A 1385 LEU cc_start: 0.9749 (tp) cc_final: 0.9524 (mm) REVERT: A 1408 MET cc_start: 0.9745 (mtm) cc_final: 0.9519 (mtp) REVERT: A 1412 MET cc_start: 0.8586 (mtm) cc_final: 0.8222 (mtp) REVERT: A 1416 MET cc_start: 0.9102 (mmt) cc_final: 0.8831 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0945 time to fit residues: 9.9377 Evaluate side-chains 56 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 119 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.041270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.031281 restraints weight = 180446.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.031800 restraints weight = 143644.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032191 restraints weight = 121320.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.032472 restraints weight = 107002.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.032666 restraints weight = 97442.276| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11701 Z= 0.133 Angle : 0.635 9.264 16300 Z= 0.328 Chirality : 0.039 0.222 1961 Planarity : 0.004 0.082 1664 Dihedral : 16.173 173.544 2513 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.32 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.25), residues: 1111 helix: 1.28 (0.21), residues: 616 sheet: -1.13 (0.56), residues: 87 loop : -1.77 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 747 TYR 0.012 0.001 TYR A1649 PHE 0.019 0.002 PHE A 846 TRP 0.025 0.002 TRP A1528 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (11701) covalent geometry : angle 0.63535 / 0.33 (16300) hydrogen bonds : bond 0.05242 / 3.61 ( 570) hydrogen bonds : angle 4.94568 / 3.56 ( 1574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.5927 (mmm) cc_final: 0.5624 (mpp) REVERT: A 548 CYS cc_start: 0.9334 (t) cc_final: 0.8605 (p) REVERT: A 712 MET cc_start: 0.9668 (ttm) cc_final: 0.9436 (mpp) REVERT: A 865 MET cc_start: 0.7571 (pmm) cc_final: 0.6596 (tpt) REVERT: A 1026 MET cc_start: 0.8954 (mpp) cc_final: 0.8596 (mpp) REVERT: A 1385 LEU cc_start: 0.9614 (tp) cc_final: 0.9400 (mm) REVERT: A 1408 MET cc_start: 0.9752 (mtm) cc_final: 0.9469 (mtp) REVERT: A 1412 MET cc_start: 0.8121 (mtm) cc_final: 0.7886 (mtp) REVERT: A 1416 MET cc_start: 0.8759 (mmt) cc_final: 0.8226 (mmm) REVERT: A 1526 MET cc_start: 0.9257 (tmm) cc_final: 0.9041 (tmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0856 time to fit residues: 10.0774 Evaluate side-chains 60 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.040299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.030367 restraints weight = 184412.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.030881 restraints weight = 145667.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.031262 restraints weight = 123001.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.031531 restraints weight = 108320.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.031738 restraints weight = 98707.362| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.7516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11701 Z= 0.157 Angle : 0.661 9.104 16300 Z= 0.342 Chirality : 0.039 0.201 1961 Planarity : 0.005 0.087 1664 Dihedral : 16.200 173.125 2513 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.40 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1111 helix: 1.20 (0.21), residues: 617 sheet: -1.22 (0.55), residues: 89 loop : -1.84 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 747 TYR 0.012 0.001 TYR A1649 PHE 0.021 0.002 PHE A 846 TRP 0.032 0.002 TRP A1528 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (11701) covalent geometry : angle 0.66063 / 0.34 (16300) hydrogen bonds : bond 0.05943 / 4.13 ( 570) hydrogen bonds : angle 5.03791 / 3.62 ( 1574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.5995 (mmm) cc_final: 0.5599 (mpp) REVERT: A 712 MET cc_start: 0.9687 (ttm) cc_final: 0.9447 (mpp) REVERT: A 865 MET cc_start: 0.7546 (pmm) cc_final: 0.6533 (tpt) REVERT: A 1026 MET cc_start: 0.9004 (mpp) cc_final: 0.8661 (mpp) REVERT: A 1200 MET cc_start: 0.5921 (ppp) cc_final: 0.4961 (ppp) REVERT: A 1385 LEU cc_start: 0.9676 (tp) cc_final: 0.9454 (mm) REVERT: A 1408 MET cc_start: 0.9773 (mtm) cc_final: 0.9489 (mtp) REVERT: A 1412 MET cc_start: 0.8232 (mtm) cc_final: 0.7980 (mtp) REVERT: A 1416 MET cc_start: 0.8793 (mmt) cc_final: 0.8262 (mmm) REVERT: A 1526 MET cc_start: 0.9320 (tmm) cc_final: 0.9086 (tmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0815 time to fit residues: 9.0333 Evaluate side-chains 55 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.040932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.030995 restraints weight = 184125.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.031519 restraints weight = 146000.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.031893 restraints weight = 123335.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032173 restraints weight = 108989.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032387 restraints weight = 99251.823| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11701 Z= 0.136 Angle : 0.634 9.030 16300 Z= 0.326 Chirality : 0.038 0.204 1961 Planarity : 0.004 0.081 1664 Dihedral : 16.052 173.519 2513 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.77 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1111 helix: 1.33 (0.21), residues: 618 sheet: -1.24 (0.56), residues: 87 loop : -1.78 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 747 TYR 0.011 0.001 TYR A1649 PHE 0.017 0.002 PHE A 846 TRP 0.023 0.002 TRP A1528 HIS 0.006 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (11701) covalent geometry : angle 0.63393 / 0.33 (16300) hydrogen bonds : bond 0.05234 / 3.57 ( 570) hydrogen bonds : angle 4.92439 / 3.54 ( 1574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.79 seconds wall clock time: 34 minutes 20.07 seconds (2060.07 seconds total)