Starting phenix.real_space_refine on Sat Oct 24 03:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10gn_75156/10_2026/10gn_75156.cif Found real_map, /net/cci-nas-00/data/ceres_data/10gn_75156/10_2026/10gn_75156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10gn_75156/10_2026/10gn_75156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10gn_75156/10_2026/10gn_75156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10gn_75156/10_2026/10gn_75156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10gn_75156/10_2026/10gn_75156.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 294 5.49 5 S 10 5.16 5 C 6639 2.51 5 N 2254 2.21 5 O 2822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12019 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2997 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 147, 2997 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P B8OG I 44 " occ=0.88 ... (21 atoms not shown) pdb=" O8 B8OG I 44 " occ=0.88 Time building chain proxies: 2.87, per 1000 atoms: 0.24 Number of scatterers: 12019 At special positions: 0 Unit cell: (76.896, 122.286, 118.014, 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 10 16.00 P 294 15.00 O 2822 8.00 N 2254 7.00 C 6639 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: 0.92 Conformation dependent library (CDL) restraints added in 346.6 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 72.5% alpha, 2.6% beta 146 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.569A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.908A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.363A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.518A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.588A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.518A pdb=" N ALA D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.975A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.825A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.533A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.435A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.611A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.214A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.749A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.438A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.290A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.110A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 395 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 373 hydrogen bonds 746 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2510 1.34 - 1.46: 4158 1.46 - 1.58: 5559 1.58 - 1.70: 585 1.70 - 1.82: 20 Bond restraints: 12832 Sorted by residual: bond pdb=" P B8OG I 44 " pdb=" O5'B8OG I 44 " ideal model delta sigma weight residual 1.708 1.560 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C5' DG I 121 " pdb=" C4' DG I 121 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 1.01e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.11e-02 8.12e+03 9.49e+00 bond pdb=" N VAL C 100 " pdb=" CA VAL C 100 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.29e+00 bond pdb=" P B8OG I 44 " pdb=" OP1B8OG I 44 " ideal model delta sigma weight residual 1.519 1.459 0.060 2.00e-02 2.50e+03 8.99e+00 ... (remaining 12827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 17955 2.46 - 4.91: 566 4.91 - 7.37: 58 7.37 - 9.82: 8 9.82 - 12.28: 3 Bond angle restraints: 18590 Sorted by residual: angle pdb=" N GLU E 97 " pdb=" CA GLU E 97 " pdb=" C GLU E 97 " ideal model delta sigma weight residual 111.28 105.85 5.43 1.09e+00 8.42e-01 2.48e+01 angle pdb=" N GLY G 105 " pdb=" CA GLY G 105 " pdb=" C GLY G 105 " ideal model delta sigma weight residual 113.18 101.49 11.69 2.37e+00 1.78e-01 2.43e+01 angle pdb=" N ASN B 25 " pdb=" CA ASN B 25 " pdb=" C ASN B 25 " ideal model delta sigma weight residual 114.64 107.15 7.49 1.52e+00 4.33e-01 2.43e+01 angle pdb=" N THR D 122 " pdb=" CA THR D 122 " pdb=" C THR D 122 " ideal model delta sigma weight residual 111.36 116.66 -5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N ALA G 70 " pdb=" CA ALA G 70 " pdb=" C ALA G 70 " ideal model delta sigma weight residual 111.28 116.52 -5.24 1.09e+00 8.42e-01 2.31e+01 ... (remaining 18585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 5357 31.64 - 63.28: 1576 63.28 - 94.93: 37 94.93 - 126.57: 0 126.57 - 158.21: 5 Dihedral angle restraints: 6975 sinusoidal: 4785 harmonic: 2190 Sorted by residual: dihedral pdb=" CD ARG H 33 " pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " pdb=" NH1 ARG H 33 " ideal model delta sinusoidal sigma weight residual 0.00 -83.86 83.86 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CD ARG G 71 " pdb=" NE ARG G 71 " pdb=" CZ ARG G 71 " pdb=" NH1 ARG G 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.69 82.69 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CD ARG H 86 " pdb=" NE ARG H 86 " pdb=" CZ ARG H 86 " pdb=" NH1 ARG H 86 " ideal model delta sinusoidal sigma weight residual 0.00 57.13 -57.13 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2021 0.117 - 0.234: 82 0.234 - 0.351: 10 0.351 - 0.468: 1 0.468 - 0.585: 2 Chirality restraints: 2116 Sorted by residual: chirality pdb=" P DG J 32 " pdb=" OP1 DG J 32 " pdb=" OP2 DG J 32 " pdb=" O5' DG J 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" P DA J 31 " pdb=" OP1 DA J 31 " pdb=" OP2 DA J 31 " pdb=" O5' DA J 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA ALA G 103 " pdb=" N ALA G 103 " pdb=" C ALA G 103 " pdb=" CB ALA G 103 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 2113 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 71 " -1.104 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG G 71 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 71 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG G 71 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG G 71 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 33 " 1.101 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG H 33 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG H 33 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 33 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 33 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 86 " -0.916 9.50e-02 1.11e+02 4.11e-01 1.02e+02 pdb=" NE ARG H 86 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG H 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 86 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 86 " -0.024 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3396 2.85 - 3.36: 10197 3.36 - 3.87: 24431 3.87 - 4.39: 27322 4.39 - 4.90: 38235 Nonbonded interactions: 103581 Sorted by model distance: nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 92 " model vdw 2.335 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.341 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.353 3.040 nonbonded pdb=" NH2 ARG E 72 " pdb=" OP1 DT J 51 " model vdw 2.395 3.120 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.406 3.120 ... (remaining 103576 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } 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=0.88 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.490 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 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 : 0.007 0.148 12832 Z= 0.600 Angle : 1.007 12.279 18590 Z= 0.810 Chirality : 0.060 0.585 2116 Planarity : 0.026 0.495 1331 Dihedral : 28.073 158.211 5563 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: 0.45 (0.29), residues: 740 helix: 0.98 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 29 TYR 0.027 0.002 TYR F 88 PHE 0.008 0.002 PHE H 70 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.60 (12832) covalent geometry : angle 1.00660 / 0.81 (18590) hydrogen bonds : bond 0.12161 / 7.90 ( 768) hydrogen bonds : angle 4.09370 / 2.89 ( 1916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8934 (mtp-110) cc_final: 0.8672 (mmm-85) REVERT: A 120 MET cc_start: 0.8875 (mtt) cc_final: 0.8583 (mtp) REVERT: B 25 ASN cc_start: 0.8802 (m-40) cc_final: 0.8556 (m-40) REVERT: C 99 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8145 (mtmt) REVERT: C 110 ASN cc_start: 0.9131 (t0) cc_final: 0.8861 (p0) REVERT: D 68 ASP cc_start: 0.8982 (t70) cc_final: 0.8752 (t0) REVERT: E 73 GLU cc_start: 0.8780 (tt0) cc_final: 0.8527 (tt0) REVERT: E 80 THR cc_start: 0.9180 (m) cc_final: 0.8850 (p) REVERT: F 25 ASN cc_start: 0.8880 (m-40) cc_final: 0.8661 (m110) REVERT: F 59 LYS cc_start: 0.9152 (tttp) cc_final: 0.8912 (tttp) REVERT: G 76 THR cc_start: 0.9358 (p) cc_final: 0.9153 (t) REVERT: H 63 ASN cc_start: 0.8693 (t0) cc_final: 0.8485 (m-40) REVERT: H 68 ASP cc_start: 0.9141 (t0) cc_final: 0.8940 (t0) REVERT: H 71 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8535 (mt-10) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.7746 time to fit residues: 168.7732 Evaluate side-chains 163 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.091492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058383 restraints weight = 27152.779| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.83 r_work: 0.2727 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12832 Z= 0.160 Angle : 0.637 7.166 18590 Z= 0.376 Chirality : 0.045 0.235 2116 Planarity : 0.005 0.069 1331 Dihedral : 30.855 152.568 4069 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.83 % Allowed : 17.38 % Favored : 78.79 % 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: 1.96 (0.31), residues: 740 helix: 2.14 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.24 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 33 TYR 0.013 0.001 TYR H 37 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (12832) covalent geometry : angle 0.63712 / 0.38 (18590) hydrogen bonds : bond 0.04640 / 3.14 ( 768) hydrogen bonds : angle 2.96718 / 2.08 ( 1916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8865 (mtp-110) cc_final: 0.8630 (mmm-85) REVERT: B 92 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8025 (ttm-80) REVERT: B 93 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: C 75 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7878 (mptt) REVERT: C 99 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8016 (mtmt) REVERT: C 110 ASN cc_start: 0.9127 (t0) cc_final: 0.8780 (p0) REVERT: D 68 ASP cc_start: 0.9054 (t70) cc_final: 0.8763 (t0) REVERT: D 105 GLU cc_start: 0.8844 (tp30) cc_final: 0.8621 (tp30) REVERT: D 116 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8539 (tppt) REVERT: F 59 LYS cc_start: 0.9062 (tttp) cc_final: 0.8780 (tttp) REVERT: G 56 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: H 33 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7514 (mmm-85) REVERT: H 34 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7620 (mppt) REVERT: H 63 ASN cc_start: 0.8599 (t0) cc_final: 0.8364 (m-40) REVERT: H 68 ASP cc_start: 0.9154 (t0) cc_final: 0.8946 (t0) REVERT: H 71 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8549 (tm-30) outliers start: 24 outliers final: 7 residues processed: 180 average time/residue: 0.7687 time to fit residues: 146.7219 Evaluate side-chains 167 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [76, 43, 18, 58, 13, 98, 94, 89, 95, 87, 79] chunk 76 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 104 GLN H 49 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.053676 restraints weight = 27486.870| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.80 r_work: 0.2586 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12832 Z= 0.322 Angle : 0.752 10.734 18590 Z= 0.414 Chirality : 0.050 0.286 2116 Planarity : 0.005 0.042 1331 Dihedral : 31.519 151.932 4069 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.58 % Allowed : 17.07 % Favored : 77.35 % 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: 2.05 (0.31), residues: 740 helix: 2.15 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 40 TYR 0.020 0.002 TYR A 54 PHE 0.018 0.002 PHE F 100 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.32 (12832) covalent geometry : angle 0.75180 / 0.41 (18590) hydrogen bonds : bond 0.05926 / 3.98 ( 768) hydrogen bonds : angle 3.02482 / 2.11 ( 1916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8705 (pt0) cc_final: 0.8258 (pt0) REVERT: A 53 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7727 (ttp-170) REVERT: B 22 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7199 (mm) REVERT: B 59 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8935 (ttmm) REVERT: B 92 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: B 93 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: C 75 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8187 (mptt) REVERT: C 99 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8229 (mtmt) REVERT: C 110 ASN cc_start: 0.9087 (t0) cc_final: 0.8766 (p0) REVERT: D 68 ASP cc_start: 0.9209 (t70) cc_final: 0.8838 (t0) REVERT: D 116 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8668 (tppt) REVERT: F 59 LYS cc_start: 0.9178 (tttp) cc_final: 0.8912 (tttm) REVERT: G 56 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: H 63 ASN cc_start: 0.8836 (t0) cc_final: 0.8507 (m-40) REVERT: H 68 ASP cc_start: 0.9199 (t0) cc_final: 0.8951 (t0) REVERT: H 71 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8709 (tm-30) outliers start: 35 outliers final: 17 residues processed: 178 average time/residue: 0.8024 time to fit residues: 151.0719 Evaluate side-chains 175 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [15, 41, 8, 37, 1, 50, 10, 70, 74, 64, 5] chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.055983 restraints weight = 27286.213| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.80 r_work: 0.2672 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12832 Z= 0.143 Angle : 0.615 9.551 18590 Z= 0.359 Chirality : 0.043 0.312 2116 Planarity : 0.004 0.038 1331 Dihedral : 31.234 149.516 4069 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.47 % Allowed : 19.62 % Favored : 75.92 % 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: 2.55 (0.31), residues: 740 helix: 2.56 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.016 0.001 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (12832) covalent geometry : angle 0.61480 / 0.36 (18590) hydrogen bonds : bond 0.03998 / 2.70 ( 768) hydrogen bonds : angle 2.71396 / 1.90 ( 1916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 80 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8962 (p) REVERT: B 92 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8294 (ttm-80) REVERT: C 99 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8056 (mtmt) REVERT: C 110 ASN cc_start: 0.9071 (t0) cc_final: 0.8740 (p0) REVERT: D 68 ASP cc_start: 0.9154 (t70) cc_final: 0.8797 (t0) REVERT: D 116 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8572 (tppt) REVERT: F 59 LYS cc_start: 0.9050 (tttp) cc_final: 0.8752 (tttm) REVERT: G 56 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: H 63 ASN cc_start: 0.8647 (t0) cc_final: 0.8323 (m-40) REVERT: H 68 ASP cc_start: 0.9163 (t0) cc_final: 0.8952 (t0) REVERT: H 71 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8572 (tm-30) outliers start: 28 outliers final: 12 residues processed: 173 average time/residue: 0.7901 time to fit residues: 144.6451 Evaluate side-chains 170 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [87, 77, 8, 49, 16, 57, 84, 70, 19, 18, 82] chunk 87 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN G 104 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055822 restraints weight = 27393.312| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.82 r_work: 0.2671 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12832 Z= 0.160 Angle : 0.616 6.769 18590 Z= 0.358 Chirality : 0.043 0.304 2116 Planarity : 0.004 0.037 1331 Dihedral : 31.198 148.596 4069 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.83 % Allowed : 22.01 % Favored : 74.16 % 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: 2.68 (0.31), residues: 740 helix: 2.64 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.016 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (12832) covalent geometry : angle 0.61601 / 0.36 (18590) hydrogen bonds : bond 0.04041 / 2.74 ( 768) hydrogen bonds : angle 2.68555 / 1.87 ( 1916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7216 (mm) REVERT: B 59 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8861 (ttpp) REVERT: B 80 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8953 (p) REVERT: B 92 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8313 (ttm-80) REVERT: C 99 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8067 (mtmt) REVERT: C 110 ASN cc_start: 0.9073 (t0) cc_final: 0.8608 (p0) REVERT: D 68 ASP cc_start: 0.9138 (t70) cc_final: 0.8791 (OUTLIER) REVERT: D 116 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8563 (tppt) REVERT: F 59 LYS cc_start: 0.9047 (tttp) cc_final: 0.8758 (tttm) REVERT: G 56 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: H 63 ASN cc_start: 0.8669 (t0) cc_final: 0.8338 (m-40) REVERT: H 68 ASP cc_start: 0.9168 (t0) cc_final: 0.8941 (t0) REVERT: H 71 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8573 (tm-30) outliers start: 24 outliers final: 10 residues processed: 169 average time/residue: 0.8104 time to fit residues: 145.0089 Evaluate side-chains 164 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [68, 49, 85, 14, 10, 84, 8, 6, 65, 5, 7] chunk 68 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 63 ASN G 104 GLN H 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.089779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056357 restraints weight = 27323.830| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.82 r_work: 0.2684 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12832 Z= 0.142 Angle : 0.607 10.345 18590 Z= 0.353 Chirality : 0.042 0.309 2116 Planarity : 0.004 0.037 1331 Dihedral : 31.150 147.714 4069 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.99 % Allowed : 21.85 % Favored : 74.16 % 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: 2.77 (0.31), residues: 740 helix: 2.70 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.020 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (12832) covalent geometry : angle 0.60661 / 0.35 (18590) hydrogen bonds : bond 0.03809 / 2.58 ( 768) hydrogen bonds : angle 2.61995 / 1.83 ( 1916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8853 (ttpp) REVERT: B 80 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8925 (p) REVERT: B 92 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8132 (ttm-80) REVERT: B 93 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: C 99 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8071 (mtmt) REVERT: C 110 ASN cc_start: 0.9064 (t0) cc_final: 0.8606 (p0) REVERT: D 68 ASP cc_start: 0.9117 (t70) cc_final: 0.8786 (t0) REVERT: D 116 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8546 (tppt) REVERT: F 59 LYS cc_start: 0.9051 (tttp) cc_final: 0.8760 (tttm) REVERT: G 56 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: H 63 ASN cc_start: 0.8650 (t0) cc_final: 0.8334 (m-40) REVERT: H 71 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8571 (tm-30) REVERT: H 76 GLU cc_start: 0.9130 (tp30) cc_final: 0.8799 (mm-30) REVERT: H 105 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6968 (tm-30) outliers start: 25 outliers final: 15 residues processed: 169 average time/residue: 0.7668 time to fit residues: 137.2685 Evaluate side-chains 170 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [11, 79, 60, 13, 94, 80, 46, 92, 19, 76, 99] chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 94 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.088272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054669 restraints weight = 27286.898| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.81 r_work: 0.2635 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12832 Z= 0.233 Angle : 0.661 8.899 18590 Z= 0.373 Chirality : 0.045 0.313 2116 Planarity : 0.004 0.038 1331 Dihedral : 31.311 147.609 4069 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.83 % Allowed : 22.17 % Favored : 74.00 % 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: 2.65 (0.31), residues: 740 helix: 2.59 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.86 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.019 0.002 TYR D 40 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (12832) covalent geometry : angle 0.66074 / 0.37 (18590) hydrogen bonds : bond 0.04517 / 3.05 ( 768) hydrogen bonds : angle 2.75425 / 1.92 ( 1916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8987 (mp10) REVERT: B 59 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8969 (ttpp) REVERT: B 92 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8181 (ttm-80) REVERT: B 93 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: B 95 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8141 (mtp85) REVERT: C 99 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8185 (mtmt) REVERT: C 110 ASN cc_start: 0.9079 (t0) cc_final: 0.8795 (p0) REVERT: D 68 ASP cc_start: 0.9184 (t70) cc_final: 0.8864 (t0) REVERT: D 116 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8657 (tppt) REVERT: F 59 LYS cc_start: 0.9127 (tttp) cc_final: 0.8852 (tttm) REVERT: G 56 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: H 63 ASN cc_start: 0.8769 (t0) cc_final: 0.8444 (m-40) REVERT: H 71 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8649 (tm-30) REVERT: H 76 GLU cc_start: 0.9149 (tp30) cc_final: 0.8844 (mm-30) outliers start: 24 outliers final: 15 residues processed: 162 average time/residue: 0.8083 time to fit residues: 138.4687 Evaluate side-chains 169 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [52, 77, 85, 79, 56, 64, 21, 81, 31, 4, 71] chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN E 68 GLN G 31 HIS G 104 GLN H 49 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056080 restraints weight = 27110.989| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.81 r_work: 0.2680 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12832 Z= 0.141 Angle : 0.611 10.894 18590 Z= 0.356 Chirality : 0.042 0.323 2116 Planarity : 0.004 0.038 1331 Dihedral : 31.166 146.319 4069 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.99 % Allowed : 22.81 % Favored : 73.21 % 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: 2.85 (0.31), residues: 740 helix: 2.75 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.021 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12832) covalent geometry : angle 0.61128 / 0.36 (18590) hydrogen bonds : bond 0.03779 / 2.56 ( 768) hydrogen bonds : angle 2.61561 / 1.82 ( 1916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8869 (ttpp) REVERT: B 80 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8918 (p) REVERT: B 92 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8254 (ttm-80) REVERT: C 99 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8087 (mtmt) REVERT: C 110 ASN cc_start: 0.9058 (t0) cc_final: 0.8753 (p0) REVERT: D 68 ASP cc_start: 0.9143 (t70) cc_final: 0.8815 (t0) REVERT: D 116 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8541 (tppt) REVERT: F 59 LYS cc_start: 0.9035 (tttp) cc_final: 0.8745 (tttm) REVERT: F 92 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8966 (ttp80) REVERT: G 56 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: H 63 ASN cc_start: 0.8651 (t0) cc_final: 0.8315 (m-40) REVERT: H 71 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8554 (tm-30) outliers start: 25 outliers final: 14 residues processed: 168 average time/residue: 0.7718 time to fit residues: 137.5204 Evaluate side-chains 168 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [23, 22, 18, 61, 37, 10, 99, 79, 55, 62, 40] chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.055998 restraints weight = 27100.623| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.82 r_work: 0.2667 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12832 Z= 0.152 Angle : 0.623 11.496 18590 Z= 0.359 Chirality : 0.042 0.316 2116 Planarity : 0.004 0.037 1331 Dihedral : 31.136 145.685 4069 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.83 % Allowed : 22.97 % Favored : 73.21 % 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: 2.85 (0.31), residues: 740 helix: 2.74 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.78 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.021 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 HIS 0.009 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (12832) covalent geometry : angle 0.62321 / 0.36 (18590) hydrogen bonds : bond 0.03943 / 2.66 ( 768) hydrogen bonds : angle 2.60962 / 1.82 ( 1916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8657 (mtp) REVERT: B 59 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8868 (ttpp) REVERT: B 80 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8910 (p) REVERT: B 92 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8164 (ttm-80) REVERT: B 93 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: C 99 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8084 (mtmt) REVERT: C 110 ASN cc_start: 0.9065 (t0) cc_final: 0.8769 (p0) REVERT: D 68 ASP cc_start: 0.9141 (t70) cc_final: 0.8817 (t0) REVERT: D 116 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8547 (tppt) REVERT: F 59 LYS cc_start: 0.9043 (tttp) cc_final: 0.8745 (tttm) REVERT: F 92 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8964 (ttp80) REVERT: G 56 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: H 63 ASN cc_start: 0.8641 (t0) cc_final: 0.8328 (m-40) REVERT: H 71 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8565 (tm-30) REVERT: H 105 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7373 (tm-30) outliers start: 24 outliers final: 13 residues processed: 163 average time/residue: 0.7887 time to fit residues: 136.2773 Evaluate side-chains 169 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [20, 78, 67, 55, 97, 92, 6, 15, 23, 87, 29] chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.055906 restraints weight = 27190.914| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.82 r_work: 0.2673 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12832 Z= 0.164 Angle : 0.629 11.435 18590 Z= 0.361 Chirality : 0.042 0.318 2116 Planarity : 0.004 0.037 1331 Dihedral : 31.147 145.359 4069 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.19 % Allowed : 23.76 % Favored : 73.05 % 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: 2.84 (0.31), residues: 740 helix: 2.73 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.75 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.022 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (12832) covalent geometry : angle 0.62854 / 0.36 (18590) hydrogen bonds : bond 0.03958 / 2.67 ( 768) hydrogen bonds : angle 2.62837 / 1.83 ( 1916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8488 (pm20) cc_final: 0.8263 (pm20) REVERT: A 120 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8662 (mtp) REVERT: B 59 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8865 (ttpp) REVERT: B 80 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8907 (p) REVERT: B 92 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8279 (ttm-80) REVERT: C 99 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8083 (mtmt) REVERT: C 110 ASN cc_start: 0.9060 (t0) cc_final: 0.8760 (p0) REVERT: D 68 ASP cc_start: 0.9147 (t70) cc_final: 0.8822 (t0) REVERT: D 108 LYS cc_start: 0.8810 (pttt) cc_final: 0.8514 (pttp) REVERT: D 116 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8549 (tppt) REVERT: E 76 GLN cc_start: 0.8710 (mt0) cc_final: 0.8359 (pt0) REVERT: F 59 LYS cc_start: 0.9042 (tttp) cc_final: 0.8748 (tttm) REVERT: F 92 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8949 (ttp80) REVERT: G 56 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: G 76 THR cc_start: 0.9418 (p) cc_final: 0.9167 (t) REVERT: H 63 ASN cc_start: 0.8657 (t0) cc_final: 0.8321 (m-40) REVERT: H 71 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8562 (tm-30) outliers start: 20 outliers final: 13 residues processed: 163 average time/residue: 0.7920 time to fit residues: 136.9330 Evaluate side-chains 169 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [94, 49, 53, 14, 20, 30, 89, 58, 41, 17, 10] chunk 94 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.089758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056259 restraints weight = 27371.407| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.84 r_work: 0.2680 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (27 function evaluations) r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12832 Z= 0.145 Angle : 0.635 13.798 18590 Z= 0.362 Chirality : 0.042 0.320 2116 Planarity : 0.004 0.037 1331 Dihedral : 31.120 145.209 4069 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.51 % Allowed : 23.76 % Favored : 72.73 % 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: 2.85 (0.31), residues: 740 helix: 2.75 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.77 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.022 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (12832) covalent geometry : angle 0.63478 / 0.36 (18590) hydrogen bonds : bond 0.03847 / 2.59 ( 768) hydrogen bonds : angle 2.61312 / 1.82 ( 1916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4324.22 seconds wall clock time: 74 minutes 17.40 seconds (4457.40 seconds total)