Starting phenix.real_space_refine on Mon Feb 10 19:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j47_35972/02_2025/8j47_35972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j47_35972/02_2025/8j47_35972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j47_35972/02_2025/8j47_35972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j47_35972/02_2025/8j47_35972.map" model { file = "/net/cci-nas-00/data/ceres_data/8j47_35972/02_2025/8j47_35972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j47_35972/02_2025/8j47_35972.cif" } resolution = 2.5 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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1350 2.51 5 N 370 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2080 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Time building chain proxies: 2.34, per 1000 atoms: 1.12 Number of scatterers: 2080 At special positions: 0 Unit cell: (72.908, 96.9345, 43.082, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 350 8.00 N 370 7.00 C 1350 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: 0.49 Conformation dependent library (CDL) restraints added in 275.4 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.687A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.250A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE F 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE H 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.241A pdb=" N VAL D 36 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 36 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL H 36 " --> pdb=" O GLY J 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.617A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.198A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.324A pdb=" N VAL C 36 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 36 " --> pdb=" O GLY G 37 " (cutoff:3.500A) 21 hydrogen bonds defined for protein. 63 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.44 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 680 1.34 - 1.46: 366 1.46 - 1.57: 1044 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2110 Sorted by residual: bond pdb=" C ILE E 32 " pdb=" N GLY E 33 " ideal model delta sigma weight residual 1.335 1.326 0.010 1.19e-02 7.06e+03 6.43e-01 bond pdb=" CA VAL E 39 " pdb=" CB VAL E 39 " ideal model delta sigma weight residual 1.542 1.550 -0.008 1.08e-02 8.57e+03 5.74e-01 bond pdb=" C ILE A 32 " pdb=" N GLY A 33 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.19e-02 7.06e+03 5.70e-01 bond pdb=" C ILE I 32 " pdb=" N GLY I 33 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.19e-02 7.06e+03 5.55e-01 bond pdb=" C ILE G 32 " pdb=" N GLY G 33 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.19e-02 7.06e+03 5.51e-01 ... (remaining 2105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 2712 1.35 - 2.69: 72 2.69 - 4.04: 31 4.04 - 5.39: 10 5.39 - 6.73: 5 Bond angle restraints: 2830 Sorted by residual: angle pdb=" N VAL G 39 " pdb=" CA VAL G 39 " pdb=" C VAL G 39 " ideal model delta sigma weight residual 112.43 105.70 6.73 9.20e-01 1.18e+00 5.36e+01 angle pdb=" N VAL C 39 " pdb=" CA VAL C 39 " pdb=" C VAL C 39 " ideal model delta sigma weight residual 112.43 105.70 6.73 9.20e-01 1.18e+00 5.35e+01 angle pdb=" N VAL A 39 " pdb=" CA VAL A 39 " pdb=" C VAL A 39 " ideal model delta sigma weight residual 112.43 105.70 6.73 9.20e-01 1.18e+00 5.35e+01 angle pdb=" N VAL E 39 " pdb=" CA VAL E 39 " pdb=" C VAL E 39 " ideal model delta sigma weight residual 112.43 105.72 6.71 9.20e-01 1.18e+00 5.32e+01 angle pdb=" N VAL I 39 " pdb=" CA VAL I 39 " pdb=" C VAL I 39 " ideal model delta sigma weight residual 112.43 105.72 6.71 9.20e-01 1.18e+00 5.32e+01 ... (remaining 2825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 989 16.13 - 32.27: 96 32.27 - 48.40: 60 48.40 - 64.53: 10 64.53 - 80.66: 5 Dihedral angle restraints: 1160 sinusoidal: 420 harmonic: 740 Sorted by residual: dihedral pdb=" CB LYS C 28 " pdb=" CG LYS C 28 " pdb=" CD LYS C 28 " pdb=" CE LYS C 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS G 28 " pdb=" CG LYS G 28 " pdb=" CD LYS G 28 " pdb=" CE LYS G 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS A 28 " pdb=" CG LYS A 28 " pdb=" CD LYS A 28 " pdb=" CE LYS A 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 127 0.026 - 0.052: 118 0.052 - 0.078: 20 0.078 - 0.104: 8 0.104 - 0.130: 57 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA VAL E 39 " pdb=" N VAL E 39 " pdb=" C VAL E 39 " pdb=" CB VAL E 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL C 39 " pdb=" N VAL C 39 " pdb=" C VAL C 39 " pdb=" CB VAL C 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 327 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 39 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C VAL E 39 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL E 39 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 40 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 39 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C VAL C 39 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL C 39 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 40 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 39 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C VAL G 39 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL G 39 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL G 40 " 0.009 2.00e-02 2.50e+03 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1094 2.99 - 3.47: 1676 3.47 - 3.95: 3313 3.95 - 4.42: 3216 4.42 - 4.90: 6634 Nonbonded interactions: 15933 Sorted by model distance: nonbonded pdb=" N VAL A 39 " pdb=" N VAL A 40 " model vdw 2.518 2.560 nonbonded pdb=" N VAL G 39 " pdb=" N VAL G 40 " model vdw 2.518 2.560 nonbonded pdb=" N VAL C 39 " pdb=" N VAL C 40 " model vdw 2.518 2.560 nonbonded pdb=" N VAL E 39 " pdb=" N VAL E 40 " model vdw 2.519 2.560 nonbonded pdb=" N VAL I 39 " pdb=" N VAL I 40 " model vdw 2.519 2.560 ... (remaining 15928 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.160 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 0.028 2110 Z= 0.279 Angle : 0.737 6.733 2830 Z= 0.501 Chirality : 0.057 0.130 330 Planarity : 0.003 0.016 360 Dihedral : 18.268 80.665 700 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.38 % Allowed : 30.95 % Favored : 66.67 % 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: -2.51 (0.49), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 13 PHE 0.013 0.003 PHE E 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.274 Fit side-chains REVERT: D 23 ASP cc_start: 0.7156 (m-30) cc_final: 0.6747 (m-30) REVERT: C 15 GLN cc_start: 0.7463 (pp30) cc_final: 0.7243 (tt0) REVERT: C 23 ASP cc_start: 0.7337 (m-30) cc_final: 0.7133 (m-30) REVERT: F 23 ASP cc_start: 0.7125 (m-30) cc_final: 0.6693 (m-30) REVERT: E 15 GLN cc_start: 0.7541 (pp30) cc_final: 0.7255 (tt0) REVERT: E 26 SER cc_start: 0.8320 (p) cc_final: 0.8018 (p) REVERT: B 23 ASP cc_start: 0.7459 (m-30) cc_final: 0.7233 (m-30) REVERT: A 15 GLN cc_start: 0.7582 (pp30) cc_final: 0.7363 (tm-30) REVERT: A 23 ASP cc_start: 0.7520 (m-30) cc_final: 0.7262 (m-30) REVERT: A 34 LEU cc_start: 0.8117 (tt) cc_final: 0.7744 (tt) REVERT: J 35 MET cc_start: 0.7580 (ttp) cc_final: 0.7373 (ttm) REVERT: I 40 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6776 (p) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.8749 time to fit residues: 55.6842 Evaluate side-chains 55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 15 GLN I 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.152764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101046 restraints weight = 1784.864| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.31 r_work: 0.3240 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 2110 Z= 0.453 Angle : 0.873 8.558 2830 Z= 0.419 Chirality : 0.066 0.177 330 Planarity : 0.004 0.020 360 Dihedral : 8.164 51.098 294 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 13.33 % Allowed : 19.05 % Favored : 67.62 % 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: -2.86 (0.45), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.022 0.004 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.216 Fit side-chains REVERT: C 13 HIS cc_start: 0.4248 (OUTLIER) cc_final: 0.3974 (m-70) REVERT: C 15 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: E 13 HIS cc_start: 0.4201 (OUTLIER) cc_final: 0.3934 (m-70) REVERT: E 15 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: E 26 SER cc_start: 0.8696 (p) cc_final: 0.8469 (p) REVERT: A 13 HIS cc_start: 0.4658 (OUTLIER) cc_final: 0.4217 (m90) REVERT: A 15 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 34 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8394 (mp) REVERT: H 23 ASP cc_start: 0.7879 (m-30) cc_final: 0.7648 (m-30) REVERT: G 13 HIS cc_start: 0.4302 (OUTLIER) cc_final: 0.3826 (m-70) REVERT: I 13 HIS cc_start: 0.4747 (OUTLIER) cc_final: 0.4408 (m170) REVERT: I 16 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7345 (ptmm) REVERT: I 17 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7641 (pp) outliers start: 28 outliers final: 12 residues processed: 71 average time/residue: 0.7689 time to fit residues: 56.1842 Evaluate side-chains 77 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101799 restraints weight = 1752.136| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.32 r_work: 0.3251 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2110 Z= 0.340 Angle : 0.769 7.707 2830 Z= 0.361 Chirality : 0.060 0.136 330 Planarity : 0.003 0.015 360 Dihedral : 7.871 43.556 293 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 14.29 % Allowed : 15.71 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.04 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.017 0.003 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.226 Fit side-chains REVERT: D 13 HIS cc_start: 0.4721 (OUTLIER) cc_final: 0.4314 (m-70) REVERT: C 13 HIS cc_start: 0.4241 (OUTLIER) cc_final: 0.3991 (m-70) REVERT: C 15 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: E 15 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: E 26 SER cc_start: 0.8795 (p) cc_final: 0.8572 (p) REVERT: B 13 HIS cc_start: 0.5058 (OUTLIER) cc_final: 0.4126 (t70) REVERT: A 13 HIS cc_start: 0.4720 (OUTLIER) cc_final: 0.4312 (m-70) REVERT: A 15 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7475 (OUTLIER) REVERT: A 34 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8357 (mp) REVERT: H 23 ASP cc_start: 0.7865 (m-30) cc_final: 0.7661 (m-30) REVERT: J 13 HIS cc_start: 0.5031 (OUTLIER) cc_final: 0.4819 (m-70) REVERT: I 17 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7512 (pp) outliers start: 30 outliers final: 14 residues processed: 70 average time/residue: 0.6605 time to fit residues: 47.7768 Evaluate side-chains 78 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.153468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101301 restraints weight = 1755.936| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.28 r_work: 0.3256 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2110 Z= 0.384 Angle : 0.809 8.754 2830 Z= 0.369 Chirality : 0.062 0.138 330 Planarity : 0.003 0.019 360 Dihedral : 8.178 45.801 293 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 14.29 % Allowed : 14.76 % Favored : 70.95 % 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: -3.19 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 14 PHE 0.018 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.230 Fit side-chains REVERT: D 13 HIS cc_start: 0.4543 (OUTLIER) cc_final: 0.4178 (m-70) REVERT: C 13 HIS cc_start: 0.4412 (OUTLIER) cc_final: 0.3938 (m-70) REVERT: E 13 HIS cc_start: 0.4340 (OUTLIER) cc_final: 0.4054 (m170) REVERT: E 15 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: E 26 SER cc_start: 0.8711 (p) cc_final: 0.8492 (p) REVERT: B 13 HIS cc_start: 0.5062 (OUTLIER) cc_final: 0.4184 (t70) REVERT: A 13 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.4329 (m-70) REVERT: A 15 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7473 (OUTLIER) REVERT: A 34 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8326 (mp) REVERT: J 13 HIS cc_start: 0.5146 (OUTLIER) cc_final: 0.4915 (m-70) REVERT: I 17 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7552 (pp) outliers start: 30 outliers final: 18 residues processed: 69 average time/residue: 0.7399 time to fit residues: 52.7547 Evaluate side-chains 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.154090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.101822 restraints weight = 1754.774| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.29 r_work: 0.3258 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2110 Z= 0.322 Angle : 0.761 9.718 2830 Z= 0.344 Chirality : 0.059 0.132 330 Planarity : 0.003 0.015 360 Dihedral : 8.050 47.339 293 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 16.67 % Allowed : 16.67 % Favored : 66.67 % 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: -3.23 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.016 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.243 Fit side-chains REVERT: D 13 HIS cc_start: 0.4490 (OUTLIER) cc_final: 0.4143 (m-70) REVERT: C 13 HIS cc_start: 0.4208 (OUTLIER) cc_final: 0.3651 (m90) REVERT: E 13 HIS cc_start: 0.4355 (OUTLIER) cc_final: 0.4048 (m170) REVERT: E 15 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: B 13 HIS cc_start: 0.5031 (OUTLIER) cc_final: 0.4144 (t70) REVERT: A 13 HIS cc_start: 0.4635 (OUTLIER) cc_final: 0.4364 (m-70) REVERT: A 34 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8350 (mp) REVERT: J 13 HIS cc_start: 0.5142 (OUTLIER) cc_final: 0.4919 (m-70) REVERT: I 17 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7513 (pp) outliers start: 35 outliers final: 20 residues processed: 73 average time/residue: 0.7038 time to fit residues: 53.0546 Evaluate side-chains 83 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.154377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101950 restraints weight = 1764.683| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.30 r_work: 0.3261 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2110 Z= 0.307 Angle : 0.747 10.253 2830 Z= 0.337 Chirality : 0.058 0.132 330 Planarity : 0.003 0.014 360 Dihedral : 7.845 46.414 293 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 15.71 % Allowed : 16.19 % Favored : 68.10 % 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: -3.25 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.015 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.178 Fit side-chains REVERT: D 13 HIS cc_start: 0.4444 (OUTLIER) cc_final: 0.4097 (m-70) REVERT: C 13 HIS cc_start: 0.4209 (OUTLIER) cc_final: 0.3679 (m90) REVERT: E 13 HIS cc_start: 0.4386 (OUTLIER) cc_final: 0.4099 (m170) REVERT: B 13 HIS cc_start: 0.5061 (OUTLIER) cc_final: 0.4196 (t70) REVERT: A 13 HIS cc_start: 0.4756 (OUTLIER) cc_final: 0.4448 (m-70) REVERT: A 15 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: A 34 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8351 (mp) REVERT: I 17 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7506 (pp) outliers start: 33 outliers final: 20 residues processed: 72 average time/residue: 0.6692 time to fit residues: 49.7133 Evaluate side-chains 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.156233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104270 restraints weight = 1761.180| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.28 r_work: 0.3290 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2110 Z= 0.191 Angle : 0.638 9.631 2830 Z= 0.293 Chirality : 0.055 0.129 330 Planarity : 0.002 0.012 360 Dihedral : 7.004 39.202 293 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 11.90 % Allowed : 21.43 % Favored : 66.67 % 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: -3.23 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 14 PHE 0.013 0.002 PHE A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.240 Fit side-chains REVERT: D 13 HIS cc_start: 0.4286 (OUTLIER) cc_final: 0.3898 (m-70) REVERT: C 13 HIS cc_start: 0.4134 (OUTLIER) cc_final: 0.3649 (m90) REVERT: E 13 HIS cc_start: 0.4386 (OUTLIER) cc_final: 0.4129 (m170) REVERT: E 26 SER cc_start: 0.8752 (p) cc_final: 0.8534 (p) REVERT: A 15 GLN cc_start: 0.7727 (pt0) cc_final: 0.7396 (tt0) REVERT: A 34 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8343 (mp) REVERT: I 17 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7412 (pp) outliers start: 25 outliers final: 17 residues processed: 67 average time/residue: 0.7641 time to fit residues: 52.7856 Evaluate side-chains 75 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 0.0040 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 overall best weight: 3.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103133 restraints weight = 1871.512| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.29 r_work: 0.3285 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2110 Z= 0.358 Angle : 0.781 11.454 2830 Z= 0.353 Chirality : 0.060 0.133 330 Planarity : 0.003 0.014 360 Dihedral : 7.810 47.212 293 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 12.86 % Allowed : 20.48 % Favored : 66.67 % 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: -3.29 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.017 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.208 Fit side-chains REVERT: D 13 HIS cc_start: 0.4257 (OUTLIER) cc_final: 0.3950 (m-70) REVERT: C 13 HIS cc_start: 0.4156 (OUTLIER) cc_final: 0.3665 (m90) REVERT: E 13 HIS cc_start: 0.4459 (OUTLIER) cc_final: 0.4211 (m-70) REVERT: B 13 HIS cc_start: 0.5041 (OUTLIER) cc_final: 0.4236 (t70) REVERT: A 13 HIS cc_start: 0.4741 (OUTLIER) cc_final: 0.4433 (m-70) REVERT: A 15 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: A 34 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8343 (mp) REVERT: I 17 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7524 (pp) outliers start: 27 outliers final: 18 residues processed: 68 average time/residue: 0.7346 time to fit residues: 51.4074 Evaluate side-chains 80 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN 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 = 0.158610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103422 restraints weight = 1742.351| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.39 r_work: 0.3274 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2110 Z= 0.189 Angle : 0.649 10.389 2830 Z= 0.298 Chirality : 0.054 0.129 330 Planarity : 0.002 0.012 360 Dihedral : 7.028 40.111 293 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 11.90 % Allowed : 20.95 % Favored : 67.14 % 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: -3.21 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 14 PHE 0.016 0.003 PHE A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.219 Fit side-chains REVERT: D 13 HIS cc_start: 0.4214 (OUTLIER) cc_final: 0.3915 (m-70) REVERT: C 13 HIS cc_start: 0.4082 (OUTLIER) cc_final: 0.3629 (m90) REVERT: E 13 HIS cc_start: 0.4478 (OUTLIER) cc_final: 0.4261 (m-70) REVERT: B 13 HIS cc_start: 0.5023 (OUTLIER) cc_final: 0.4198 (t70) REVERT: A 15 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 34 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8361 (mp) REVERT: I 13 HIS cc_start: 0.4797 (OUTLIER) cc_final: 0.4489 (m170) REVERT: I 17 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7439 (pp) outliers start: 25 outliers final: 15 residues processed: 67 average time/residue: 0.7279 time to fit residues: 50.2908 Evaluate side-chains 76 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.0000 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105296 restraints weight = 1712.897| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.35 r_work: 0.3327 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2110 Z= 0.144 Angle : 0.574 9.978 2830 Z= 0.270 Chirality : 0.053 0.129 330 Planarity : 0.002 0.012 360 Dihedral : 6.374 33.333 292 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 10.00 % Allowed : 22.38 % Favored : 67.62 % 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: -3.17 (0.44), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 14 PHE 0.014 0.002 PHE C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.235 Fit side-chains REVERT: E 13 HIS cc_start: 0.4435 (OUTLIER) cc_final: 0.4232 (m170) REVERT: E 26 SER cc_start: 0.8754 (p) cc_final: 0.8540 (p) REVERT: B 13 HIS cc_start: 0.5028 (OUTLIER) cc_final: 0.4207 (t70) REVERT: A 15 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: A 34 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8348 (mp) REVERT: I 13 HIS cc_start: 0.4875 (OUTLIER) cc_final: 0.4657 (m90) REVERT: I 17 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7381 (pp) outliers start: 21 outliers final: 11 residues processed: 66 average time/residue: 0.7261 time to fit residues: 49.4246 Evaluate side-chains 71 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.155351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100389 restraints weight = 1742.145| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.35 r_work: 0.3243 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2110 Z= 0.438 Angle : 0.883 12.486 2830 Z= 0.401 Chirality : 0.063 0.148 330 Planarity : 0.003 0.018 360 Dihedral : 8.183 52.304 292 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 10.00 % Allowed : 23.33 % Favored : 66.67 % 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: -3.26 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 14 PHE 0.021 0.004 PHE J 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.82 seconds wall clock time: 41 minutes 53.81 seconds (2513.81 seconds total)