Starting phenix.real_space_refine on Sat Aug 23 10:38:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be5_44470/08_2025/9be5_44470.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be5_44470/08_2025/9be5_44470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2025/9be5_44470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2025/9be5_44470.map" model { file = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2025/9be5_44470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2025/9be5_44470.cif" } resolution = 3.3 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= 0.003 sd= 0.028 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 288 5.49 5 S 12 5.16 5 C 6576 2.51 5 N 2231 2.21 5 O 2791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11898 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.60, per 1000 atoms: 0.22 Number of scatterers: 11898 At special positions: 0 Unit cell: (73.08, 123.54, 118.32, 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 12 16.00 P 288 15.00 O 2791 8.00 N 2231 7.00 C 6576 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 427.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 73.1% alpha, 2.9% beta 128 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.746A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 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: 3.675A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.539A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.716A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.832A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (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 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.521A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.584A 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 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.769A 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: 6.478A 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: 7.442A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 'C' and resid 101 through 102 removed outlier: 6.760A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.332A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 406 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2432 1.33 - 1.45: 4054 1.45 - 1.57: 5616 1.57 - 1.69: 576 1.69 - 1.81: 22 Bond restraints: 12700 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.46e+00 bond pdb=" C6 DG J -36 " pdb=" O6 DG J -36 " ideal model delta sigma weight residual 1.239 1.219 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CB LYS C 74 " pdb=" CG LYS C 74 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.46e-01 ... (remaining 12695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17758 1.42 - 2.85: 591 2.85 - 4.27: 37 4.27 - 5.70: 13 5.70 - 7.12: 1 Bond angle restraints: 18400 Sorted by residual: angle pdb=" CB LYS C 74 " pdb=" CG LYS C 74 " pdb=" CD LYS C 74 " ideal model delta sigma weight residual 111.30 118.42 -7.12 2.30e+00 1.89e-01 9.59e+00 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 118.60 -5.42 2.37e+00 1.78e-01 5.24e+00 angle pdb=" N ARG C 17 " pdb=" CA ARG C 17 " pdb=" C ARG C 17 " ideal model delta sigma weight residual 113.23 110.45 2.78 1.24e+00 6.50e-01 5.03e+00 angle pdb=" N GLN F 27 " pdb=" CA GLN F 27 " pdb=" C GLN F 27 " ideal model delta sigma weight residual 113.01 110.34 2.67 1.20e+00 6.94e-01 4.96e+00 angle pdb=" CB GLU H 32 " pdb=" CG GLU H 32 " pdb=" CD GLU H 32 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.70e+00 3.46e-01 4.75e+00 ... (remaining 18395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 5519 35.01 - 70.02: 1347 70.02 - 105.03: 24 105.03 - 140.04: 3 140.04 - 175.05: 1 Dihedral angle restraints: 6894 sinusoidal: 4715 harmonic: 2179 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 44.95 175.05 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 81.39 138.61 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DA J -38 " pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 92.22 127.78 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 6891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1998 0.066 - 0.133: 96 0.133 - 0.199: 1 0.199 - 0.265: 0 0.265 - 0.332: 2 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CB ILE H 86 " pdb=" CA ILE H 86 " pdb=" CG1 ILE H 86 " pdb=" CG2 ILE H 86 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB ILE D 86 " pdb=" CA ILE D 86 " pdb=" CG1 ILE D 86 " pdb=" CG2 ILE D 86 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 2094 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO C 80 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.022 2.00e-02 2.50e+03 9.32e-03 2.39e+00 pdb=" N9 DA I -35 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO G 80 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 644 2.71 - 3.26: 11030 3.26 - 3.81: 23956 3.81 - 4.35: 28509 4.35 - 4.90: 41145 Nonbonded interactions: 105284 Sorted by model distance: nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.167 3.040 nonbonded pdb=" NH1 ARG D 83 " pdb=" OE2 GLU D 90 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.244 3.040 nonbonded pdb=" NE2 GLN G 24 " pdb=" OE1 GLN H 44 " model vdw 2.269 3.120 ... (remaining 105279 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.360 Find NCS groups from input model: 0.270 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12700 Z= 0.167 Angle : 0.581 7.123 18400 Z= 0.360 Chirality : 0.034 0.332 2097 Planarity : 0.004 0.044 1325 Dihedral : 28.066 175.051 5488 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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 aren not related in a simple way. whole: 1.53 (0.30), residues: 735 helix: 1.65 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.74 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.014 0.001 TYR C 57 PHE 0.026 0.002 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00357 (12700) covalent geometry : angle 0.58089 (18400) hydrogen bonds : bond 0.11947 ( 733) hydrogen bonds : angle 4.73008 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.196 Fit side-chains REVERT: C 33 LEU cc_start: 0.8149 (mt) cc_final: 0.7915 (mt) REVERT: D 56 MET cc_start: 0.7779 (tpp) cc_final: 0.7440 (mmm) REVERT: H 59 MET cc_start: 0.8332 (mmp) cc_final: 0.7877 (mmp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1234 time to fit residues: 10.8176 Evaluate side-chains 53 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN E 108 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.185748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122569 restraints weight = 13884.538| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.62 r_work: 0.3293 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12700 Z= 0.159 Angle : 0.563 10.870 18400 Z= 0.334 Chirality : 0.033 0.147 2097 Planarity : 0.004 0.042 1325 Dihedral : 31.182 176.888 4008 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.44 % Allowed : 3.84 % Favored : 94.72 % 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 aren not related in a simple way. whole: 2.26 (0.30), residues: 735 helix: 2.16 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.48 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.015 0.001 TYR H 80 PHE 0.016 0.001 PHE C 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00352 (12700) covalent geometry : angle 0.56300 (18400) hydrogen bonds : bond 0.04004 ( 733) hydrogen bonds : angle 2.82465 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.339 Fit side-chains REVERT: A 133 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6990 (mt-10) REVERT: C 72 ASP cc_start: 0.7427 (m-30) cc_final: 0.7178 (m-30) REVERT: E 81 ASP cc_start: 0.8497 (t0) cc_final: 0.8208 (t0) REVERT: H 118 TYR cc_start: 0.7408 (t80) cc_final: 0.7175 (t80) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.1236 time to fit residues: 11.5439 Evaluate side-chains 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126773 restraints weight = 13361.479| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.66 r_work: 0.3307 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12700 Z= 0.155 Angle : 0.542 10.389 18400 Z= 0.322 Chirality : 0.032 0.154 2097 Planarity : 0.004 0.039 1325 Dihedral : 31.118 179.760 4008 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.44 % Allowed : 6.24 % Favored : 92.32 % 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 aren not related in a simple way. whole: 2.54 (0.30), residues: 735 helix: 2.38 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.014 0.001 TYR C 57 PHE 0.016 0.001 PHE C 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (12700) covalent geometry : angle 0.54245 (18400) hydrogen bonds : bond 0.03728 ( 733) hydrogen bonds : angle 2.69112 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.276 Fit side-chains REVERT: A 56 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6211 (mttt) REVERT: A 133 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6888 (mt-10) REVERT: C 72 ASP cc_start: 0.7279 (m-30) cc_final: 0.7008 (m-30) REVERT: C 74 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7111 (mtmm) REVERT: G 19 SER cc_start: 0.7422 (m) cc_final: 0.6918 (p) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.1351 time to fit residues: 11.5128 Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.188937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127344 restraints weight = 13282.062| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.66 r_work: 0.3290 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12700 Z= 0.149 Angle : 0.536 11.471 18400 Z= 0.317 Chirality : 0.032 0.157 2097 Planarity : 0.003 0.039 1325 Dihedral : 31.002 176.827 4008 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.12 % Allowed : 7.36 % Favored : 91.52 % 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 aren not related in a simple way. whole: 2.69 (0.30), residues: 735 helix: 2.46 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.25 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.013 0.001 TYR C 57 PHE 0.015 0.001 PHE C 25 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00329 (12700) covalent geometry : angle 0.53611 (18400) hydrogen bonds : bond 0.03599 ( 733) hydrogen bonds : angle 2.60522 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.322 Fit side-chains REVERT: A 56 LYS cc_start: 0.7348 (ttpt) cc_final: 0.6339 (mttt) REVERT: A 80 THR cc_start: 0.8637 (p) cc_final: 0.8406 (m) REVERT: A 133 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6953 (mt-10) REVERT: G 19 SER cc_start: 0.7513 (m) cc_final: 0.7012 (p) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.1438 time to fit residues: 11.8033 Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 46 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.188265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126775 restraints weight = 13348.293| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.66 r_work: 0.3276 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12700 Z= 0.158 Angle : 0.535 11.437 18400 Z= 0.316 Chirality : 0.032 0.159 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.018 176.619 4008 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.12 % Allowed : 8.32 % Favored : 90.56 % 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 aren not related in a simple way. whole: 2.69 (0.30), residues: 735 helix: 2.47 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.28 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.020 0.001 TYR H 118 PHE 0.012 0.001 PHE C 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00356 (12700) covalent geometry : angle 0.53510 (18400) hydrogen bonds : bond 0.03609 ( 733) hydrogen bonds : angle 2.60961 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.280 Fit side-chains REVERT: A 56 LYS cc_start: 0.7354 (ttpt) cc_final: 0.6320 (mttt) REVERT: A 80 THR cc_start: 0.8640 (p) cc_final: 0.8408 (m) REVERT: A 133 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6957 (mt-10) REVERT: C 72 ASP cc_start: 0.7271 (m-30) cc_final: 0.7014 (m-30) REVERT: G 19 SER cc_start: 0.7508 (m) cc_final: 0.7005 (p) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1210 time to fit residues: 10.1318 Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.188424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126850 restraints weight = 13386.221| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.67 r_work: 0.3289 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12700 Z= 0.151 Angle : 0.535 12.482 18400 Z= 0.315 Chirality : 0.032 0.150 2097 Planarity : 0.003 0.041 1325 Dihedral : 30.997 176.417 4008 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.12 % Allowed : 8.96 % Favored : 89.92 % 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 aren not related in a simple way. whole: 2.80 (0.30), residues: 735 helix: 2.54 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.21 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.017 0.001 TYR H 118 PHE 0.012 0.001 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (12700) covalent geometry : angle 0.53466 (18400) hydrogen bonds : bond 0.03556 ( 733) hydrogen bonds : angle 2.57891 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.219 Fit side-chains REVERT: A 56 LYS cc_start: 0.7346 (ttpt) cc_final: 0.6313 (mttt) REVERT: A 80 THR cc_start: 0.8672 (p) cc_final: 0.8445 (m) REVERT: A 133 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6985 (mt-10) REVERT: C 74 LYS cc_start: 0.7510 (mmmm) cc_final: 0.7000 (mtmm) REVERT: G 19 SER cc_start: 0.7504 (m) cc_final: 0.6996 (p) outliers start: 7 outliers final: 7 residues processed: 56 average time/residue: 0.1237 time to fit residues: 9.7529 Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.187000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125091 restraints weight = 13333.134| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.66 r_work: 0.3254 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12700 Z= 0.177 Angle : 0.552 12.693 18400 Z= 0.322 Chirality : 0.033 0.148 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.076 176.403 4008 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.44 % Allowed : 9.44 % Favored : 89.12 % 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 aren not related in a simple way. whole: 2.60 (0.30), residues: 735 helix: 2.41 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.32 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.013 0.001 TYR C 57 PHE 0.014 0.001 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00406 (12700) covalent geometry : angle 0.55186 (18400) hydrogen bonds : bond 0.03707 ( 733) hydrogen bonds : angle 2.65756 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.304 Fit side-chains REVERT: A 56 LYS cc_start: 0.7334 (ttpt) cc_final: 0.6296 (mttt) REVERT: A 80 THR cc_start: 0.8681 (p) cc_final: 0.8451 (m) REVERT: A 133 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 74 LYS cc_start: 0.7487 (mmmm) cc_final: 0.6995 (mtmm) REVERT: G 19 SER cc_start: 0.7523 (m) cc_final: 0.7013 (p) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1241 time to fit residues: 10.5219 Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.188106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126497 restraints weight = 13306.692| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.65 r_work: 0.3295 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12700 Z= 0.152 Angle : 0.540 12.629 18400 Z= 0.315 Chirality : 0.032 0.154 2097 Planarity : 0.003 0.041 1325 Dihedral : 31.010 176.036 4008 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.12 % Allowed : 9.76 % Favored : 89.12 % 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 aren not related in a simple way. whole: 2.75 (0.30), residues: 735 helix: 2.51 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.22 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.012 0.001 TYR G 57 PHE 0.009 0.001 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00340 (12700) covalent geometry : angle 0.53984 (18400) hydrogen bonds : bond 0.03553 ( 733) hydrogen bonds : angle 2.58270 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.344 Fit side-chains REVERT: A 56 LYS cc_start: 0.7375 (ttpt) cc_final: 0.6341 (mttt) REVERT: A 80 THR cc_start: 0.8696 (p) cc_final: 0.8468 (m) REVERT: A 133 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6975 (mt-10) REVERT: C 33 LEU cc_start: 0.8239 (mt) cc_final: 0.8013 (mt) REVERT: C 74 LYS cc_start: 0.7452 (mmmm) cc_final: 0.6978 (mtmm) REVERT: G 19 SER cc_start: 0.7536 (m) cc_final: 0.7026 (p) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.1078 time to fit residues: 9.0722 Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.184480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121959 restraints weight = 13262.056| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.64 r_work: 0.3207 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12700 Z= 0.199 Angle : 0.584 13.369 18400 Z= 0.334 Chirality : 0.034 0.144 2097 Planarity : 0.004 0.039 1325 Dihedral : 31.340 176.379 4008 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.28 % Allowed : 10.72 % Favored : 88.00 % 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 aren not related in a simple way. whole: 2.32 (0.30), residues: 735 helix: 2.19 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.33 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.014 0.002 TYR C 57 PHE 0.016 0.002 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00465 (12700) covalent geometry : angle 0.58397 (18400) hydrogen bonds : bond 0.03907 ( 733) hydrogen bonds : angle 2.80185 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.259 Fit side-chains REVERT: A 56 LYS cc_start: 0.7148 (ttpt) cc_final: 0.6061 (mttt) REVERT: A 80 THR cc_start: 0.8676 (p) cc_final: 0.8465 (m) REVERT: A 133 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7002 (mt-10) REVERT: G 19 SER cc_start: 0.7511 (m) cc_final: 0.7011 (p) outliers start: 8 outliers final: 7 residues processed: 68 average time/residue: 0.1054 time to fit residues: 10.3279 Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 0.0050 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.189372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128220 restraints weight = 13291.774| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.65 r_work: 0.3323 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12700 Z= 0.141 Angle : 0.540 12.262 18400 Z= 0.315 Chirality : 0.032 0.140 2097 Planarity : 0.003 0.041 1325 Dihedral : 30.957 176.003 4008 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.28 % Allowed : 10.72 % Favored : 88.00 % 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 aren not related in a simple way. whole: 2.92 (0.30), residues: 735 helix: 2.59 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.03 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.012 0.001 TYR H 80 PHE 0.011 0.001 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00304 (12700) covalent geometry : angle 0.54033 (18400) hydrogen bonds : bond 0.03460 ( 733) hydrogen bonds : angle 2.52580 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.282 Fit side-chains REVERT: A 56 LYS cc_start: 0.7269 (ttpt) cc_final: 0.6221 (mttt) REVERT: A 80 THR cc_start: 0.8677 (p) cc_final: 0.8467 (m) REVERT: C 74 LYS cc_start: 0.7501 (mmmm) cc_final: 0.6991 (mtmm) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.1023 time to fit residues: 8.9706 Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.189136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127570 restraints weight = 13299.488| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.68 r_work: 0.3303 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12700 Z= 0.142 Angle : 0.535 12.382 18400 Z= 0.314 Chirality : 0.032 0.133 2097 Planarity : 0.003 0.042 1325 Dihedral : 30.984 175.806 4008 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.44 % Allowed : 11.04 % Favored : 87.52 % 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 aren not related in a simple way. whole: 2.97 (0.30), residues: 735 helix: 2.64 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.04 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.031 0.001 TYR H 80 PHE 0.011 0.001 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00309 (12700) covalent geometry : angle 0.53517 (18400) hydrogen bonds : bond 0.03456 ( 733) hydrogen bonds : angle 2.54110 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.73 seconds wall clock time: 39 minutes 30.18 seconds (2370.18 seconds total)