Starting phenix.real_space_refine on Fri Sep 11 20:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eld_31181/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eld_31181/09_2026/7eld_31181.map" } 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-2.2.1-6174/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: {'RNAv2': 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: 2.21, 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 480.8 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: 1.24 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: 2.87 Time building geometry restraints manager: 1.13 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 - 2.06: 13195 2.06 - 4.11: 3000 4.11 - 6.17: 91 6.17 - 8.23: 12 8.23 - 10.28: 2 Bond angle restraints: 16300 Sorted by residual: 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 angle pdb=" CA HIS A 874 " pdb=" C HIS A 874 " pdb=" O HIS A 874 " ideal model delta sigma weight residual 120.51 113.39 7.12 1.43e+00 4.89e-01 2.48e+01 ... (remaining 16295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 6425 35.28 - 70.55: 433 70.55 - 105.83: 4 105.83 - 141.10: 0 141.10 - 176.38: 1 Dihedral angle restraints: 6863 sinusoidal: 3537 harmonic: 3326 Sorted by residual: dihedral pdb=" C4' C B 116 " pdb=" C3' C B 116 " pdb=" C2' C B 116 " pdb=" C1' C B 116 " ideal model delta sinusoidal sigma weight residual 36.35 -34.03 70.37 1 3.10e+00 1.04e-01 6.63e+02 dihedral pdb=" C4' A B 54 " pdb=" C3' A B 54 " pdb=" C2' A B 54 " pdb=" C1' A B 54 " ideal model delta sinusoidal sigma weight residual 36.34 -33.39 69.74 1 3.10e+00 1.04e-01 6.53e+02 dihedral pdb=" C4' G B 36 " pdb=" C3' G B 36 " pdb=" C2' G B 36 " pdb=" C1' G B 36 " ideal model delta sinusoidal sigma weight residual 36.34 -33.16 69.50 1 3.10e+00 1.04e-01 6.49e+02 ... (remaining 6860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1078 0.101 - 0.202: 733 0.202 - 0.302: 141 0.302 - 0.403: 8 0.403 - 0.504: 1 Chirality restraints: 1961 Sorted by residual: 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 chirality pdb=" CA ASP A 563 " pdb=" N ASP A 563 " pdb=" C ASP A 563 " pdb=" CB ASP A 563 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.360 Find NCS groups from input model: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- 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= 0.893 Angle : 1.441 10.284 16300 Z= 1.076 Chirality : 0.119 0.504 1961 Planarity : 0.005 0.059 1664 Dihedral : 18.549 176.377 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 0.01154 / 0.89 (11701) covalent geometry : angle 1.44126 / 1.08 (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 : 0.269 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: 0.1039 time to fit residues: 32.5172 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 : 0.290 ------------------------------------------------------------------------------- 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: 20.0000 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.046146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.035381 restraints weight = 173315.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.036024 restraints weight = 135947.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.036463 restraints weight = 113205.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.036817 restraints weight = 98969.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.036980 restraints weight = 89261.583| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11701 Z= 0.214 Angle : 0.955 10.472 16300 Z= 0.433 Chirality : 0.063 0.691 1961 Planarity : 0.005 0.068 1664 Dihedral : 15.787 166.431 2513 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.52 % Favored : 97.03 % Rotamer: Outliers : 0.51 % Allowed : 3.66 % Favored : 95.83 % 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: 1.19 (0.24), residues: 1111 helix: 2.10 (0.19), residues: 623 sheet: -0.36 (0.57), residues: 71 loop : -1.06 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1788 TYR 0.032 0.002 TYR A1513 PHE 0.025 0.003 PHE A1372 TRP 0.027 0.003 TRP A1528 HIS 0.007 0.002 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (11701) covalent geometry : angle 0.95524 / 0.43 (16300) hydrogen bonds : bond 0.06476 / 4.43 ( 570) hydrogen bonds : angle 4.97622 / 3.59 ( 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 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.336 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 865 MET cc_start: 0.7540 (pmm) cc_final: 0.6796 (tpp) REVERT: A 1408 MET cc_start: 0.9765 (mtm) cc_final: 0.9451 (mtp) REVERT: A 1416 MET cc_start: 0.8749 (mmt) cc_final: 0.8221 (mmm) outliers start: 5 outliers final: 1 residues processed: 92 average time/residue: 0.1158 time to fit residues: 15.0121 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 : 0.333 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.0170 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 overall best weight: 2.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS A 293 GLN A 433 ASN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 HIS A1582 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.046017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.035285 restraints weight = 172225.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.035910 restraints weight = 135533.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.036371 restraints weight = 113387.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.036684 restraints weight = 99032.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.036823 restraints weight = 89808.331| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4390 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= 0.145 Angle : 0.802 11.664 16300 Z= 0.361 Chirality : 0.056 0.639 1961 Planarity : 0.005 0.092 1664 Dihedral : 15.543 169.142 2513 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.60 % Favored : 96.04 % Rotamer: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1111 helix: 1.75 (0.20), residues: 619 sheet: -0.42 (0.55), residues: 86 loop : -1.09 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 763 TYR 0.017 0.001 TYR A1593 PHE 0.020 0.002 PHE A 846 TRP 0.021 0.002 TRP A 341 HIS 0.005 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (11701) covalent geometry : angle 0.80151 / 0.36 (16300) hydrogen bonds : bond 0.05561 / 3.83 ( 570) hydrogen bonds : angle 4.68606 / 3.39 ( 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 88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.301 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: A 474 LEU cc_start: 0.9375 (mm) cc_final: 0.9099 (pp) REVERT: A 865 MET cc_start: 0.7562 (pmm) cc_final: 0.6538 (tpp) REVERT: A 1026 MET cc_start: 0.8920 (mpp) cc_final: 0.8682 (mpp) REVERT: A 1408 MET cc_start: 0.9750 (mtm) cc_final: 0.9401 (ptp) REVERT: A 1412 MET cc_start: 0.8153 (mtm) cc_final: 0.7868 (mtp) REVERT: A 1416 MET cc_start: 0.8704 (mmt) cc_final: 0.8179 (mmm) outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.0978 time to fit residues: 12.5605 Evaluate side-chains 63 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 111 optimal weight: 40.0000 chunk 96 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 333 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN A1606 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.041371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.031204 restraints weight = 185762.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.031708 restraints weight = 148859.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032104 restraints weight = 126429.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.032376 restraints weight = 111277.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.032575 restraints weight = 101591.737| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11701 Z= 0.223 Angle : 0.915 11.973 16300 Z= 0.421 Chirality : 0.057 0.624 1961 Planarity : 0.006 0.101 1664 Dihedral : 15.832 171.686 2513 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 32.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.32 % Favored : 95.32 % Rotamer: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.52 % 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 (0.24), residues: 1111 helix: 1.20 (0.20), residues: 614 sheet: -0.68 (0.51), residues: 93 loop : -1.48 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 694 TYR 0.021 0.002 TYR A 771 PHE 0.037 0.003 PHE A1372 TRP 0.027 0.003 TRP A1528 HIS 0.009 0.002 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (11701) covalent geometry : angle 0.91470 / 0.42 (16300) hydrogen bonds : bond 0.07751 / 5.36 ( 570) hydrogen bonds : angle 5.07765 / 3.68 ( 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 73 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.377 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 369 MET cc_start: 0.4749 (mtt) cc_final: 0.4431 (mtp) REVERT: A 474 LEU cc_start: 0.9320 (mm) cc_final: 0.9002 (pp) REVERT: A 847 TYR cc_start: 0.8820 (t80) cc_final: 0.8536 (t80) REVERT: A 1026 MET cc_start: 0.8951 (mpp) cc_final: 0.8725 (mpp) REVERT: A 1064 MET cc_start: 0.8892 (mmm) cc_final: 0.8450 (mmm) REVERT: A 1385 LEU cc_start: 0.9677 (tp) cc_final: 0.9450 (mm) REVERT: A 1408 MET cc_start: 0.9746 (mtm) cc_final: 0.9426 (mtp) REVERT: A 1412 MET cc_start: 0.8313 (mtm) cc_final: 0.7930 (mtp) REVERT: A 1416 MET cc_start: 0.8880 (mmt) cc_final: 0.8364 (mmm) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.0941 time to fit residues: 10.2606 Evaluate side-chains 55 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 40.0000 chunk 108 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** A1606 HIS ** 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 = 0.3406 r_free = 0.3406 target = 0.042842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.032498 restraints weight = 179090.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.033040 restraints weight = 143025.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.033442 restraints weight = 120895.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.033740 restraints weight = 106543.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.033970 restraints weight = 96890.078| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11701 Z= 0.149 Angle : 0.804 11.953 16300 Z= 0.363 Chirality : 0.054 0.609 1961 Planarity : 0.005 0.090 1664 Dihedral : 15.929 175.880 2513 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.23 % Favored : 95.41 % Rotamer: Outliers : 0.10 % Allowed : 2.54 % 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: 0.33 (0.25), residues: 1111 helix: 1.39 (0.20), residues: 614 sheet: -0.77 (0.50), residues: 93 loop : -1.36 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 694 TYR 0.020 0.002 TYR A 771 PHE 0.017 0.002 PHE A 846 TRP 0.020 0.002 TRP A 341 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (11701) covalent geometry : angle 0.80356 / 0.36 (16300) hydrogen bonds : bond 0.05557 / 3.73 ( 570) hydrogen bonds : angle 4.82481 / 3.50 ( 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 76 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.7457 (ptp) cc_final: 0.7106 (ptp) REVERT: A 474 LEU cc_start: 0.9316 (mm) cc_final: 0.8990 (pp) REVERT: A 865 MET cc_start: 0.7416 (pmm) cc_final: 0.6328 (tpp) REVERT: A 1026 MET cc_start: 0.8929 (mpp) cc_final: 0.8689 (mpp) REVERT: A 1064 MET cc_start: 0.8880 (mmm) cc_final: 0.8476 (mmm) REVERT: A 1385 LEU cc_start: 0.9660 (tp) cc_final: 0.9457 (mm) REVERT: A 1408 MET cc_start: 0.9766 (mtm) cc_final: 0.9460 (mtp) REVERT: A 1412 MET cc_start: 0.8361 (mtm) cc_final: 0.7975 (mtp) REVERT: A 1416 MET cc_start: 0.8941 (mmt) cc_final: 0.8441 (mmm) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.0939 time to fit residues: 10.7952 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 : 0.387 ------------------------------------------------------------------------------- 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: 20.0000 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 122 optimal weight: 40.0000 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 77 optimal weight: 0.0570 overall best weight: 2.1102 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.043723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.033359 restraints weight = 178583.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.033924 restraints weight = 141715.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.034313 restraints weight = 119759.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.034634 restraints weight = 106077.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034865 restraints weight = 96228.823| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11701 Z= 0.128 Angle : 0.783 11.254 16300 Z= 0.351 Chirality : 0.053 0.654 1961 Planarity : 0.004 0.079 1664 Dihedral : 15.776 178.695 2513 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.14 % Favored : 95.50 % Rotamer: Outliers : 0.10 % Allowed : 1.63 % Favored : 98.27 % 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: 0.48 (0.25), residues: 1111 helix: 1.52 (0.21), residues: 613 sheet: -0.66 (0.52), residues: 91 loop : -1.34 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 747 TYR 0.016 0.001 TYR A 847 PHE 0.035 0.002 PHE A1372 TRP 0.021 0.001 TRP A 341 HIS 0.006 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (11701) covalent geometry : angle 0.78316 / 0.35 (16300) hydrogen bonds : bond 0.05084 / 3.36 ( 570) hydrogen bonds : angle 4.66329 / 3.42 ( 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 76 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9325 (mm) cc_final: 0.9010 (pp) REVERT: A 774 MET cc_start: 0.8108 (mpp) cc_final: 0.7769 (mpp) REVERT: A 865 MET cc_start: 0.7487 (pmm) cc_final: 0.6462 (mmm) REVERT: A 1064 MET cc_start: 0.8900 (mmm) cc_final: 0.8544 (mmm) REVERT: A 1408 MET cc_start: 0.9761 (mtm) cc_final: 0.9458 (mtp) REVERT: A 1412 MET cc_start: 0.8292 (mtm) cc_final: 0.7995 (mtp) REVERT: A 1416 MET cc_start: 0.8898 (mmt) cc_final: 0.8404 (mmm) REVERT: A 1526 MET cc_start: 0.9163 (tmm) cc_final: 0.8941 (tmm) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1000 time to fit residues: 11.3483 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 : 0.258 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.042195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.032012 restraints weight = 182988.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.032553 restraints weight = 145670.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.032949 restraints weight = 122673.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.033220 restraints weight = 107930.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.033450 restraints weight = 98647.101| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6495 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= 0.150 Angle : 0.797 10.560 16300 Z= 0.360 Chirality : 0.053 0.656 1961 Planarity : 0.004 0.082 1664 Dihedral : 15.867 178.433 2513 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.50 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 0.30 (0.25), residues: 1111 helix: 1.49 (0.21), residues: 608 sheet: -0.89 (0.52), residues: 93 loop : -1.53 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 747 TYR 0.012 0.001 TYR A1649 PHE 0.025 0.002 PHE A 846 TRP 0.018 0.002 TRP A 547 HIS 0.006 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (11701) covalent geometry : angle 0.79738 / 0.36 (16300) hydrogen bonds : bond 0.05748 / 3.84 ( 570) hydrogen bonds : angle 4.74877 / 3.44 ( 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 72 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9320 (mm) cc_final: 0.8984 (pp) REVERT: A 865 MET cc_start: 0.7499 (pmm) cc_final: 0.6362 (tpp) REVERT: A 1026 MET cc_start: 0.8909 (mpp) cc_final: 0.8655 (mpp) REVERT: A 1064 MET cc_start: 0.8924 (mmm) cc_final: 0.8584 (mmm) REVERT: A 1408 MET cc_start: 0.9757 (mtm) cc_final: 0.9449 (mtp) REVERT: A 1412 MET cc_start: 0.8292 (mtm) cc_final: 0.8058 (mtp) REVERT: A 1416 MET cc_start: 0.8901 (mmt) cc_final: 0.8387 (mmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0819 time to fit residues: 9.0516 Evaluate side-chains 54 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 20.0000 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 40.0000 chunk 5 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.041554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.031439 restraints weight = 182698.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031994 restraints weight = 143032.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.032408 restraints weight = 119541.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.032619 restraints weight = 104411.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.032897 restraints weight = 95693.112| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.6952 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= 0.152 Angle : 0.793 9.645 16300 Z= 0.358 Chirality : 0.052 0.681 1961 Planarity : 0.004 0.079 1664 Dihedral : 16.019 178.555 2513 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.22 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 0.26 (0.25), residues: 1111 helix: 1.41 (0.21), residues: 614 sheet: -0.79 (0.53), residues: 93 loop : -1.54 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 747 TYR 0.013 0.001 TYR A1514 PHE 0.023 0.002 PHE A 846 TRP 0.022 0.002 TRP A1528 HIS 0.007 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (11701) covalent geometry : angle 0.79321 / 0.36 (16300) hydrogen bonds : bond 0.05621 / 3.73 ( 570) hydrogen bonds : angle 4.78483 / 3.47 ( 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 73 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.3995 (mtp) cc_final: 0.3435 (mtp) REVERT: A 375 LEU cc_start: 0.9462 (tp) cc_final: 0.9177 (tp) REVERT: A 548 CYS cc_start: 0.9382 (t) cc_final: 0.8374 (p) REVERT: A 737 LEU cc_start: 0.7733 (pt) cc_final: 0.7480 (mt) REVERT: A 865 MET cc_start: 0.7507 (pmm) cc_final: 0.6331 (tpt) REVERT: A 1064 MET cc_start: 0.8925 (mmm) cc_final: 0.8619 (mmm) REVERT: A 1408 MET cc_start: 0.9775 (mtm) cc_final: 0.9461 (mtp) REVERT: A 1412 MET cc_start: 0.8373 (mtm) cc_final: 0.8029 (mtp) REVERT: A 1416 MET cc_start: 0.8896 (mmt) cc_final: 0.8394 (mmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0799 time to fit residues: 9.0062 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 : 0.244 ------------------------------------------------------------------------------- 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: 0.0770 chunk 13 optimal weight: 0.0030 chunk 119 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 overall best weight: 1.3808 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.043108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.032821 restraints weight = 176434.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.033393 restraints weight = 138849.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.033821 restraints weight = 116417.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034100 restraints weight = 101587.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.034350 restraints weight = 92462.971| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6922 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= 0.124 Angle : 0.768 9.734 16300 Z= 0.345 Chirality : 0.052 0.729 1961 Planarity : 0.004 0.068 1664 Dihedral : 15.878 178.439 2513 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.59 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 (0.25), residues: 1111 helix: 1.52 (0.21), residues: 613 sheet: -0.70 (0.55), residues: 91 loop : -1.49 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 368 TYR 0.013 0.001 TYR A1649 PHE 0.023 0.001 PHE A 556 TRP 0.017 0.001 TRP A 341 HIS 0.009 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (11701) covalent geometry : angle 0.76819 / 0.34 (16300) hydrogen bonds : bond 0.05023 / 3.32 ( 570) hydrogen bonds : angle 4.65607 / 3.38 ( 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 73 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.380 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: 0.9386 (mm) cc_final: 0.9056 (pp) REVERT: A 579 LEU cc_start: 0.9758 (tt) cc_final: 0.9530 (mm) REVERT: A 865 MET cc_start: 0.7407 (pmm) cc_final: 0.6310 (tpt) REVERT: A 1026 MET cc_start: 0.8909 (mpp) cc_final: 0.8602 (mpp) REVERT: A 1064 MET cc_start: 0.8905 (mmm) cc_final: 0.8598 (mmm) REVERT: A 1408 MET cc_start: 0.9754 (mtm) cc_final: 0.9464 (mtp) REVERT: A 1416 MET cc_start: 0.8795 (mmt) cc_final: 0.8298 (mmm) REVERT: A 1526 MET cc_start: 0.9273 (tmm) cc_final: 0.9039 (tmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0855 time to fit residues: 9.7771 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 : 0.315 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** A 546 GLN ** 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 = 0.3335 r_free = 0.3335 target = 0.040358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.030523 restraints weight = 185456.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.031007 restraints weight = 148695.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.031360 restraints weight = 126529.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.031616 restraints weight = 112358.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.031821 restraints weight = 102992.607| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11701 Z= 0.183 Angle : 0.851 9.310 16300 Z= 0.389 Chirality : 0.053 0.693 1961 Planarity : 0.005 0.080 1664 Dihedral : 16.130 178.255 2513 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 27.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.58 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.08 (0.25), residues: 1111 helix: 1.33 (0.21), residues: 607 sheet: -1.18 (0.52), residues: 98 loop : -1.61 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 368 TYR 0.015 0.002 TYR A1514 PHE 0.022 0.002 PHE A1372 TRP 0.039 0.003 TRP A1528 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (11701) covalent geometry : angle 0.85083 / 0.39 (16300) hydrogen bonds : bond 0.06875 / 4.68 ( 570) hydrogen bonds : angle 4.97952 / 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 70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 MET cc_start: 0.8064 (mpp) cc_final: 0.7623 (mpp) REVERT: A 865 MET cc_start: 0.7518 (pmm) cc_final: 0.6400 (tpt) REVERT: A 1064 MET cc_start: 0.8880 (mmm) cc_final: 0.8555 (mmm) REVERT: A 1200 MET cc_start: 0.5662 (ppp) cc_final: 0.4703 (ppp) REVERT: A 1206 MET cc_start: 0.4816 (ptt) cc_final: 0.4585 (pmm) REVERT: A 1408 MET cc_start: 0.9763 (mtm) cc_final: 0.9477 (mtp) REVERT: A 1412 MET cc_start: 0.8185 (mtm) cc_final: 0.7973 (mtm) REVERT: A 1416 MET cc_start: 0.8820 (mmt) cc_final: 0.8329 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0976 time to fit residues: 10.6215 Evaluate side-chains 53 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.041007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.030949 restraints weight = 183963.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.031500 restraints weight = 143633.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.031910 restraints weight = 120195.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.032197 restraints weight = 105092.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.032393 restraints weight = 95244.860| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11701 Z= 0.146 Angle : 0.798 9.583 16300 Z= 0.361 Chirality : 0.052 0.727 1961 Planarity : 0.004 0.079 1664 Dihedral : 16.176 178.584 2513 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.86 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.17 (0.25), residues: 1111 helix: 1.37 (0.21), residues: 614 sheet: -0.92 (0.56), residues: 89 loop : -1.63 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 368 TYR 0.014 0.001 TYR A1514 PHE 0.019 0.002 PHE A 301 TRP 0.030 0.002 TRP A1528 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (11701) covalent geometry : angle 0.79814 / 0.36 (16300) hydrogen bonds : bond 0.05697 / 3.80 ( 570) hydrogen bonds : angle 4.86954 / 3.53 ( 1574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.41 seconds wall clock time: 37 minutes 35.50 seconds (2255.50 seconds total)