Starting phenix.real_space_refine on Wed May 14 07:02:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be5_44470/05_2025/9be5_44470.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be5_44470/05_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_44470/05_2025/9be5_44470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be5_44470/05_2025/9be5_44470.map" model { file = "/net/cci-nas-00/data/ceres_data/9be5_44470/05_2025/9be5_44470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be5_44470/05_2025/9be5_44470.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.99, per 1000 atoms: 0.67 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: 2.95 Conformation dependent library (CDL) restraints added in 913.2 milliseconds 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: 6.18 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: 4.68 Time building geometry restraints manager: 3.48 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.090 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.001 HIS F 75 PHE 0.026 0.002 PHE C 25 TYR 0.014 0.001 TYR C 57 ARG 0.004 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.11947 ( 733) hydrogen bonds : angle 4.73008 ( 1854) covalent geometry : bond 0.00357 (12700) covalent geometry : angle 0.58089 (18400) *********************** 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 : 0.805 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: 0.2720 time to fit residues: 24.0051 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.184854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121456 restraints weight = 13752.473| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.60 r_work: 0.3280 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1098 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= 0.169 Angle : 0.569 11.168 18400 Z= 0.337 Chirality : 0.033 0.144 2097 Planarity : 0.004 0.042 1325 Dihedral : 31.234 176.865 4008 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.28 % Allowed : 3.84 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.30), residues: 735 helix: 2.07 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.53 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.021 0.002 PHE C 25 TYR 0.015 0.001 TYR H 80 ARG 0.004 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 733) hydrogen bonds : angle 2.87136 ( 1854) covalent geometry : bond 0.00383 (12700) covalent geometry : angle 0.56899 (18400) *********************** 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 71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.892 Fit side-chains REVERT: A 133 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7022 (mt-10) REVERT: E 81 ASP cc_start: 0.8515 (t0) cc_final: 0.8220 (t0) REVERT: H 118 TYR cc_start: 0.7387 (t80) cc_final: 0.7177 (t80) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.2982 time to fit residues: 27.0284 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 : 0.829 ------------------------------------------------------------------------------- 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 72 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ** 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 = 0.4171 r_free = 0.4171 target = 0.179532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114386 restraints weight = 13699.994| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.64 r_work: 0.3177 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12700 Z= 0.240 Angle : 0.624 11.490 18400 Z= 0.360 Chirality : 0.036 0.152 2097 Planarity : 0.005 0.038 1325 Dihedral : 31.696 178.467 4008 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.60 % Allowed : 7.04 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.30), residues: 735 helix: 1.74 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.028 0.002 PHE C 25 TYR 0.017 0.002 TYR C 57 ARG 0.005 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 733) hydrogen bonds : angle 3.05076 ( 1854) covalent geometry : bond 0.00566 (12700) covalent geometry : angle 0.62447 (18400) *********************** 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 74 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.852 Fit side-chains REVERT: C 33 LEU cc_start: 0.8518 (mt) cc_final: 0.8293 (mt) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.2873 time to fit residues: 27.3124 Evaluate side-chains 65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 E residue 56 LYS Chi-restraints excluded: chain F residue 30 THR 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 34 optimal weight: 0.0020 chunk 14 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.4646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.188137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126832 restraints weight = 13157.094| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.66 r_work: 0.3269 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12700 Z= 0.145 Angle : 0.538 11.420 18400 Z= 0.320 Chirality : 0.032 0.154 2097 Planarity : 0.004 0.042 1325 Dihedral : 31.039 177.643 4008 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.28 % Allowed : 8.96 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.31), residues: 735 helix: 2.37 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.42 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.012 0.001 PHE C 25 TYR 0.012 0.001 TYR G 57 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 733) hydrogen bonds : angle 2.60156 ( 1854) covalent geometry : bond 0.00314 (12700) covalent geometry : angle 0.53835 (18400) *********************** 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 73 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.809 Fit side-chains REVERT: A 56 LYS cc_start: 0.7224 (ttpt) cc_final: 0.6162 (mttt) REVERT: A 80 THR cc_start: 0.8681 (p) cc_final: 0.8446 (m) REVERT: B 74 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8052 (mt-10) REVERT: C 74 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7145 (mtmm) REVERT: E 90 MET cc_start: 0.7540 (tpp) cc_final: 0.7291 (mmm) REVERT: G 19 SER cc_start: 0.7431 (m) cc_final: 0.6942 (p) REVERT: H 56 MET cc_start: 0.7553 (tpp) cc_final: 0.6896 (tpp) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.2835 time to fit residues: 26.3991 Evaluate side-chains 65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 D residue 93 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.187920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126529 restraints weight = 13180.971| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.66 r_work: 0.3282 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.003 0.037 12700 Z= 0.147 Angle : 0.535 11.790 18400 Z= 0.318 Chirality : 0.032 0.150 2097 Planarity : 0.003 0.042 1325 Dihedral : 31.079 177.078 4008 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.60 % Allowed : 9.12 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.30), residues: 735 helix: 2.45 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.013 0.001 PHE C 25 TYR 0.012 0.001 TYR G 57 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 733) hydrogen bonds : angle 2.58898 ( 1854) covalent geometry : bond 0.00323 (12700) covalent geometry : angle 0.53548 (18400) *********************** 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 70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.921 Fit side-chains REVERT: A 56 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6254 (mttt) REVERT: A 80 THR cc_start: 0.8695 (p) cc_final: 0.8459 (m) REVERT: B 74 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 90 MET cc_start: 0.7779 (tpp) cc_final: 0.7543 (mmm) REVERT: G 19 SER cc_start: 0.7518 (m) cc_final: 0.7018 (p) REVERT: G 23 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6102 (mt) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.2466 time to fit residues: 22.8077 Evaluate side-chains 65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 E residue 56 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 23 LEU 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 67 optimal weight: 0.1980 chunk 89 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.186858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125177 restraints weight = 13299.469| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.66 r_work: 0.3274 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2130 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= 0.162 Angle : 0.547 11.999 18400 Z= 0.322 Chirality : 0.032 0.152 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.132 176.603 4008 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.76 % Allowed : 9.60 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 735 helix: 2.43 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE C 25 TYR 0.013 0.001 TYR C 57 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 733) hydrogen bonds : angle 2.62275 ( 1854) covalent geometry : bond 0.00364 (12700) covalent geometry : angle 0.54659 (18400) *********************** 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 70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.804 Fit side-chains REVERT: A 56 LYS cc_start: 0.7347 (ttpt) cc_final: 0.6317 (mttt) REVERT: A 80 THR cc_start: 0.8692 (p) cc_final: 0.8453 (m) REVERT: C 74 LYS cc_start: 0.7546 (mmmm) cc_final: 0.7048 (mtmm) REVERT: E 90 MET cc_start: 0.7790 (tpp) cc_final: 0.7300 (mmt) REVERT: G 19 SER cc_start: 0.7525 (m) cc_final: 0.7019 (p) REVERT: G 23 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6162 (mt) REVERT: H 56 MET cc_start: 0.7594 (tpp) cc_final: 0.6954 (tpp) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.2470 time to fit residues: 22.9280 Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 E residue 56 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 23 LEU 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 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123589 restraints weight = 13273.133| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.66 r_work: 0.3226 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2198 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= 0.176 Angle : 0.556 12.279 18400 Z= 0.325 Chirality : 0.033 0.151 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.203 176.590 4008 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.92 % Allowed : 9.60 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.30), residues: 735 helix: 2.33 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE C 25 TYR 0.014 0.001 TYR C 57 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 733) hydrogen bonds : angle 2.68657 ( 1854) covalent geometry : bond 0.00405 (12700) covalent geometry : angle 0.55622 (18400) *********************** 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 70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.888 Fit side-chains REVERT: A 56 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6260 (mttt) REVERT: A 80 THR cc_start: 0.8690 (p) cc_final: 0.8454 (m) REVERT: C 74 LYS cc_start: 0.7506 (mmmm) cc_final: 0.7035 (mtmm) REVERT: E 90 MET cc_start: 0.7756 (tpp) cc_final: 0.7291 (mmt) REVERT: F 25 ASN cc_start: 0.5628 (OUTLIER) cc_final: 0.5282 (p0) REVERT: G 19 SER cc_start: 0.7492 (m) cc_final: 0.6993 (p) REVERT: H 56 MET cc_start: 0.7577 (tpp) cc_final: 0.6515 (tpp) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.2703 time to fit residues: 24.2367 Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 124 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.183126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120590 restraints weight = 13411.204| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.65 r_work: 0.3209 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12700 Z= 0.206 Angle : 0.587 12.636 18400 Z= 0.337 Chirality : 0.035 0.150 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.460 176.370 4008 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.76 % Allowed : 10.40 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 735 helix: 2.10 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE C 25 TYR 0.015 0.002 TYR C 57 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 733) hydrogen bonds : angle 2.86076 ( 1854) covalent geometry : bond 0.00481 (12700) covalent geometry : angle 0.58729 (18400) *********************** 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 77 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.917 Fit side-chains REVERT: A 56 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6070 (mttt) REVERT: A 80 THR cc_start: 0.8682 (p) cc_final: 0.8469 (m) REVERT: C 33 LEU cc_start: 0.8342 (mt) cc_final: 0.8072 (mt) REVERT: C 74 LYS cc_start: 0.7611 (mmmm) cc_final: 0.7135 (mtmm) REVERT: E 90 MET cc_start: 0.7626 (tpp) cc_final: 0.7356 (mmm) REVERT: G 19 SER cc_start: 0.7545 (m) cc_final: 0.7052 (p) REVERT: H 56 MET cc_start: 0.7634 (tpp) cc_final: 0.6501 (tpp) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.2705 time to fit residues: 27.6244 Evaluate side-chains 71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 E residue 56 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.185720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123887 restraints weight = 13351.534| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.66 r_work: 0.3254 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12700 Z= 0.159 Angle : 0.546 12.123 18400 Z= 0.319 Chirality : 0.032 0.139 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.187 175.907 4008 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.92 % Allowed : 11.68 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.30), residues: 735 helix: 2.35 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.35 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE C 25 TYR 0.013 0.001 TYR G 57 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 733) hydrogen bonds : angle 2.65923 ( 1854) covalent geometry : bond 0.00359 (12700) covalent geometry : angle 0.54608 (18400) *********************** 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 74 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.848 Fit side-chains REVERT: A 56 LYS cc_start: 0.7280 (ttpt) cc_final: 0.6215 (mttt) REVERT: A 80 THR cc_start: 0.8694 (p) cc_final: 0.8481 (m) REVERT: E 90 MET cc_start: 0.7569 (tpp) cc_final: 0.7299 (mmm) REVERT: G 19 SER cc_start: 0.7533 (m) cc_final: 0.7029 (p) REVERT: H 56 MET cc_start: 0.7612 (tpp) cc_final: 0.6574 (tpp) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.2745 time to fit residues: 26.6912 Evaluate side-chains 67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 E residue 56 LYS Chi-restraints excluded: chain E residue 124 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.184751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122676 restraints weight = 13243.630| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.66 r_work: 0.3260 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12700 Z= 0.181 Angle : 0.564 12.699 18400 Z= 0.327 Chirality : 0.033 0.141 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.260 176.131 4008 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.92 % Allowed : 12.00 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.30), residues: 735 helix: 2.28 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.34 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE C 25 TYR 0.014 0.001 TYR C 57 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 733) hydrogen bonds : angle 2.72377 ( 1854) covalent geometry : bond 0.00418 (12700) covalent geometry : angle 0.56365 (18400) ********************** 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 73 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.774 Fit side-chains REVERT: A 56 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6216 (mttt) REVERT: A 80 THR cc_start: 0.8696 (p) cc_final: 0.8475 (m) REVERT: E 90 MET cc_start: 0.7630 (tpp) cc_final: 0.7360 (mmm) REVERT: G 19 SER cc_start: 0.7573 (m) cc_final: 0.7061 (p) REVERT: H 56 MET cc_start: 0.7643 (tpp) cc_final: 0.6585 (tpp) outliers start: 12 outliers final: 11 residues processed: 67 average time/residue: 0.2580 time to fit residues: 24.6109 Evaluate side-chains 69 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 124 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 73 ASN F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.186292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124703 restraints weight = 13170.559| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.65 r_work: 0.3273 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12700 Z= 0.156 Angle : 0.553 12.530 18400 Z= 0.321 Chirality : 0.032 0.135 2097 Planarity : 0.003 0.040 1325 Dihedral : 31.184 175.947 4008 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.24 % Allowed : 12.00 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 735 helix: 2.40 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.28 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.010 0.001 PHE C 25 TYR 0.013 0.001 TYR G 57 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 733) hydrogen bonds : angle 2.65209 ( 1854) covalent geometry : bond 0.00350 (12700) covalent geometry : angle 0.55284 (18400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.62 seconds wall clock time: 85 minutes 14.70 seconds (5114.70 seconds total)