Starting phenix.real_space_refine on Fri Aug 22 12:37:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j47_35972/08_2025/8j47_35972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j47_35972/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j47_35972/08_2025/8j47_35972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j47_35972/08_2025/8j47_35972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j47_35972/08_2025/8j47_35972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j47_35972/08_2025/8j47_35972.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.54, per 1000 atoms: 0.26 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: 0.15 Conformation dependent library (CDL) restraints added in 59.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.05 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: 0.15 Time building geometry restraints manager: 0.19 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: 0.00 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:5.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- 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= 0.188 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (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 PHE 0.013 0.003 PHE E 19 HIS 0.001 0.000 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 2110) covalent geometry : angle 0.73706 ( 2830) hydrogen bonds : bond 0.17996 ( 21) hydrogen bonds : angle 7.56948 ( 63) *********************** 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 : 0.047 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: 0.7244 (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 23 ASP cc_start: 0.7520 (m-30) cc_final: 0.7261 (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: 0.3071 time to fit residues: 19.5075 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 : 0.045 ------------------------------------------------------------------------------- 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 12 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4152 r_free = 0.4152 target = 0.151961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.100063 restraints weight = 1796.048| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.32 r_work: 0.3223 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 2110 Z= 0.362 Angle : 0.953 10.284 2830 Z= 0.450 Chirality : 0.071 0.214 330 Planarity : 0.005 0.023 360 Dihedral : 8.820 55.944 294 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 14.29 % Allowed : 18.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.44), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.005 PHE J 20 HIS 0.007 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00830 ( 2110) covalent geometry : angle 0.95332 ( 2830) hydrogen bonds : bond 0.04048 ( 21) hydrogen bonds : angle 6.43656 ( 63) *********************** 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 92 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.085 Fit side-chains REVERT: D 13 HIS cc_start: 0.4822 (OUTLIER) cc_final: 0.4063 (m-70) REVERT: C 13 HIS cc_start: 0.4396 (OUTLIER) cc_final: 0.4056 (m-70) REVERT: C 15 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: E 13 HIS cc_start: 0.4250 (OUTLIER) cc_final: 0.3951 (m-70) REVERT: E 15 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: E 26 SER cc_start: 0.8705 (p) cc_final: 0.8478 (p) REVERT: A 13 HIS cc_start: 0.4528 (OUTLIER) cc_final: 0.4095 (m90) REVERT: H 23 ASP cc_start: 0.7891 (m-30) cc_final: 0.7686 (m-30) REVERT: G 13 HIS cc_start: 0.4314 (OUTLIER) cc_final: 0.3849 (m-70) REVERT: J 13 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4887 (m-70) REVERT: I 13 HIS cc_start: 0.4766 (OUTLIER) cc_final: 0.4407 (m170) REVERT: I 16 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7398 (tttt) REVERT: I 17 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7657 (pp) outliers start: 30 outliers final: 13 residues processed: 76 average time/residue: 0.3678 time to fit residues: 28.7236 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS 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 17 LEU 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 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 13 HIS 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 Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.157757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105673 restraints weight = 1790.109| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.31 r_work: 0.3315 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2110 Z= 0.111 Angle : 0.580 6.453 2830 Z= 0.283 Chirality : 0.054 0.126 330 Planarity : 0.002 0.013 360 Dihedral : 6.664 34.772 294 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 9.05 % Allowed : 19.52 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.44), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE E 20 HIS 0.002 0.000 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2110) covalent geometry : angle 0.57957 ( 2830) hydrogen bonds : bond 0.02295 ( 21) hydrogen bonds : angle 5.69285 ( 63) *********************** 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 76 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.081 Fit side-chains REVERT: E 15 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: E 26 SER cc_start: 0.8828 (p) cc_final: 0.8594 (p) REVERT: B 13 HIS cc_start: 0.4967 (OUTLIER) cc_final: 0.4045 (t70) outliers start: 19 outliers final: 9 residues processed: 64 average time/residue: 0.3592 time to fit residues: 23.6622 Evaluate side-chains 65 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain J 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 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.152337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099979 restraints weight = 1781.771| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.30 r_work: 0.3228 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 2110 Z= 0.380 Angle : 0.993 12.297 2830 Z= 0.450 Chirality : 0.071 0.200 330 Planarity : 0.004 0.021 360 Dihedral : 8.947 60.908 292 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 13.81 % Allowed : 14.76 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (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 PHE 0.025 0.004 PHE J 20 HIS 0.012 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00862 ( 2110) covalent geometry : angle 0.99296 ( 2830) hydrogen bonds : bond 0.03686 ( 21) hydrogen bonds : angle 6.42882 ( 63) *********************** 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 84 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 0.102 Fit side-chains REVERT: D 13 HIS cc_start: 0.4734 (OUTLIER) cc_final: 0.4303 (m-70) REVERT: C 13 HIS cc_start: 0.4467 (OUTLIER) cc_final: 0.3996 (m170) REVERT: E 15 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: B 13 HIS cc_start: 0.5105 (OUTLIER) cc_final: 0.4277 (t70) REVERT: A 13 HIS cc_start: 0.4756 (OUTLIER) cc_final: 0.4313 (m90) REVERT: J 13 HIS cc_start: 0.5061 (OUTLIER) cc_final: 0.4577 (m-70) REVERT: I 17 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7520 (pp) outliers start: 29 outliers final: 16 residues processed: 71 average time/residue: 0.4004 time to fit residues: 29.2257 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 : 0.089 ------------------------------------------------------------------------------- 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 26 SER 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 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 A residue 13 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN 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 = 0.156932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104823 restraints weight = 1755.746| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.28 r_work: 0.3297 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2891 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= 0.118 Angle : 0.616 7.256 2830 Z= 0.290 Chirality : 0.054 0.126 330 Planarity : 0.002 0.010 360 Dihedral : 6.835 38.388 292 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 11.43 % Allowed : 20.00 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE J 20 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2110) covalent geometry : angle 0.61647 ( 2830) hydrogen bonds : bond 0.02117 ( 21) hydrogen bonds : angle 5.80909 ( 63) *********************** 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 83 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.087 Fit side-chains REVERT: D 13 HIS cc_start: 0.4381 (OUTLIER) cc_final: 0.4086 (m-70) REVERT: C 13 HIS cc_start: 0.4194 (OUTLIER) cc_final: 0.3652 (m90) REVERT: E 13 HIS cc_start: 0.4352 (OUTLIER) cc_final: 0.4078 (m170) REVERT: B 13 HIS cc_start: 0.5025 (OUTLIER) cc_final: 0.4133 (t70) REVERT: A 13 HIS cc_start: 0.4623 (OUTLIER) cc_final: 0.4156 (m-70) REVERT: I 17 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7287 (pp) outliers start: 24 outliers final: 12 residues processed: 71 average time/residue: 0.3362 time to fit residues: 24.6116 Evaluate side-chains 73 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.154055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103633 restraints weight = 1839.407| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.26 r_work: 0.3286 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2110 Z= 0.215 Angle : 0.752 8.395 2830 Z= 0.352 Chirality : 0.059 0.131 330 Planarity : 0.003 0.017 360 Dihedral : 7.742 46.957 292 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 13.33 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.43), 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 PHE 0.017 0.003 PHE J 20 HIS 0.005 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 2110) covalent geometry : angle 0.75234 ( 2830) hydrogen bonds : bond 0.02776 ( 21) hydrogen bonds : angle 6.05572 ( 63) *********************** 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 83 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.084 Fit side-chains REVERT: D 13 HIS cc_start: 0.4318 (OUTLIER) cc_final: 0.3994 (m-70) REVERT: C 13 HIS cc_start: 0.4270 (OUTLIER) cc_final: 0.3865 (m-70) REVERT: E 13 HIS cc_start: 0.4466 (OUTLIER) cc_final: 0.4197 (m170) REVERT: B 13 HIS cc_start: 0.5052 (OUTLIER) cc_final: 0.4234 (t70) REVERT: A 13 HIS cc_start: 0.4559 (OUTLIER) cc_final: 0.4239 (m-70) REVERT: I 17 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7397 (pp) outliers start: 28 outliers final: 18 residues processed: 68 average time/residue: 0.3203 time to fit residues: 22.4483 Evaluate side-chains 78 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.047 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.152610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100083 restraints weight = 1751.664| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.30 r_work: 0.3219 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 2110 Z= 0.342 Angle : 0.959 11.845 2830 Z= 0.436 Chirality : 0.067 0.188 330 Planarity : 0.004 0.017 360 Dihedral : 8.514 54.057 292 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 12.38 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.004 PHE J 20 HIS 0.008 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00769 ( 2110) covalent geometry : angle 0.95948 ( 2830) hydrogen bonds : bond 0.03401 ( 21) hydrogen bonds : angle 6.27753 ( 63) *********************** 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: 26 poor density : 54 time to evaluate : 0.053 Fit side-chains REVERT: D 13 HIS cc_start: 0.4496 (OUTLIER) cc_final: 0.4147 (m-70) REVERT: C 13 HIS cc_start: 0.4331 (OUTLIER) cc_final: 0.3892 (m170) REVERT: E 13 HIS cc_start: 0.4678 (OUTLIER) cc_final: 0.4420 (m-70) REVERT: B 13 HIS cc_start: 0.5089 (OUTLIER) cc_final: 0.4243 (t70) REVERT: A 13 HIS cc_start: 0.4714 (OUTLIER) cc_final: 0.4262 (m-70) REVERT: I 17 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7492 (pp) outliers start: 26 outliers final: 17 residues processed: 68 average time/residue: 0.3456 time to fit residues: 24.1752 Evaluate side-chains 74 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain H 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.158066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102764 restraints weight = 1711.558| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.36 r_work: 0.3259 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2110 Z= 0.148 Angle : 0.682 8.969 2830 Z= 0.317 Chirality : 0.056 0.134 330 Planarity : 0.002 0.012 360 Dihedral : 7.326 41.935 292 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 11.43 % Allowed : 21.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE J 19 HIS 0.004 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2110) covalent geometry : angle 0.68180 ( 2830) hydrogen bonds : bond 0.02418 ( 21) hydrogen bonds : angle 5.94221 ( 63) *********************** 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 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.081 Fit side-chains REVERT: D 13 HIS cc_start: 0.4112 (OUTLIER) cc_final: 0.3842 (m-70) REVERT: C 13 HIS cc_start: 0.4186 (OUTLIER) cc_final: 0.3686 (m90) REVERT: E 13 HIS cc_start: 0.4661 (OUTLIER) cc_final: 0.4349 (m-70) REVERT: B 13 HIS cc_start: 0.5011 (OUTLIER) cc_final: 0.4193 (t70) REVERT: A 13 HIS cc_start: 0.4583 (OUTLIER) cc_final: 0.4049 (m-70) REVERT: I 17 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7360 (pp) outliers start: 24 outliers final: 16 residues processed: 71 average time/residue: 0.2957 time to fit residues: 21.6619 Evaluate side-chains 76 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.047 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain H 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.153255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101251 restraints weight = 1774.098| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.29 r_work: 0.3244 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 2110 Z= 0.310 Angle : 0.912 10.824 2830 Z= 0.421 Chirality : 0.065 0.163 330 Planarity : 0.004 0.018 360 Dihedral : 8.334 51.434 292 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 11.90 % Allowed : 20.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.004 PHE J 20 HIS 0.007 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 2110) covalent geometry : angle 0.91233 ( 2830) hydrogen bonds : bond 0.03235 ( 21) hydrogen bonds : angle 6.20210 ( 63) *********************** 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 : 0.046 Fit side-chains REVERT: D 13 HIS cc_start: 0.4264 (OUTLIER) cc_final: 0.3976 (m-70) REVERT: C 13 HIS cc_start: 0.4316 (OUTLIER) cc_final: 0.3782 (m90) REVERT: B 13 HIS cc_start: 0.5116 (OUTLIER) cc_final: 0.4293 (t70) REVERT: A 13 HIS cc_start: 0.4713 (OUTLIER) cc_final: 0.4304 (m-70) REVERT: I 13 HIS cc_start: 0.4924 (OUTLIER) cc_final: 0.4473 (m170) REVERT: I 17 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7463 (pp) outliers start: 25 outliers final: 15 residues processed: 69 average time/residue: 0.2217 time to fit residues: 15.7453 Evaluate side-chains 74 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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 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 40 VAL Chi-restraints excluded: chain H 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 8 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.157332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102201 restraints weight = 1757.630| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.35 r_work: 0.3266 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2110 Z= 0.151 Angle : 0.718 9.530 2830 Z= 0.335 Chirality : 0.056 0.134 330 Planarity : 0.002 0.013 360 Dihedral : 7.299 41.356 292 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 9.52 % Allowed : 21.90 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE C 19 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2110) covalent geometry : angle 0.71844 ( 2830) hydrogen bonds : bond 0.02358 ( 21) hydrogen bonds : angle 5.87451 ( 63) ********************** 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 76 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.070 Fit side-chains REVERT: D 13 HIS cc_start: 0.4074 (OUTLIER) cc_final: 0.3851 (m-70) REVERT: C 13 HIS cc_start: 0.4176 (OUTLIER) cc_final: 0.3641 (m90) REVERT: B 13 HIS cc_start: 0.5083 (OUTLIER) cc_final: 0.4252 (t70) REVERT: A 13 HIS cc_start: 0.4747 (OUTLIER) cc_final: 0.4194 (m-70) REVERT: A 17 LEU cc_start: 0.7695 (pt) cc_final: 0.7384 (mp) REVERT: I 13 HIS cc_start: 0.4784 (OUTLIER) cc_final: 0.4411 (m170) REVERT: I 17 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7359 (pp) outliers start: 20 outliers final: 14 residues processed: 67 average time/residue: 0.2251 time to fit residues: 15.5114 Evaluate side-chains 74 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.044 ------------------------------------------------------------------------------- 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 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 13 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H 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 14 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.157417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102002 restraints weight = 1765.637| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.37 r_work: 0.3262 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2110 Z= 0.147 Angle : 0.692 9.557 2830 Z= 0.324 Chirality : 0.056 0.133 330 Planarity : 0.003 0.016 360 Dihedral : 7.274 40.873 292 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 9.52 % Allowed : 22.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE C 19 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2110) covalent geometry : angle 0.69197 ( 2830) hydrogen bonds : bond 0.02334 ( 21) hydrogen bonds : angle 5.87955 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.79 seconds wall clock time: 20 minutes 2.56 seconds (1202.56 seconds total)