Starting phenix.real_space_refine on Wed Nov 13 23:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j47_35972/11_2024/8j47_35972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j47_35972/11_2024/8j47_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j47_35972/11_2024/8j47_35972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j47_35972/11_2024/8j47_35972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j47_35972/11_2024/8j47_35972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j47_35972/11_2024/8j47_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-5513/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: 2.25, per 1000 atoms: 1.08 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: 0.46 Conformation dependent library (CDL) restraints added in 261.1 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: 0.29 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: 0.41 Time building geometry restraints manager: 0.55 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: 1.220 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.080 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- 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 : 0.210 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: 0.9119 time to fit residues: 58.0099 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 : 0.233 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.268 Fit side-chains REVERT: D 23 ASP cc_start: 0.7126 (m-30) cc_final: 0.6873 (m-30) REVERT: C 13 HIS cc_start: 0.3851 (OUTLIER) cc_final: 0.3552 (m-70) REVERT: C 15 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: E 13 HIS cc_start: 0.3843 (OUTLIER) cc_final: 0.3538 (m-70) REVERT: E 15 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: E 26 SER cc_start: 0.8211 (p) cc_final: 0.7894 (p) REVERT: B 23 ASP cc_start: 0.7726 (m-30) cc_final: 0.7482 (m-30) REVERT: A 13 HIS cc_start: 0.4211 (OUTLIER) cc_final: 0.3765 (m90) REVERT: A 15 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: A 34 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7536 (mp) REVERT: H 23 ASP cc_start: 0.7128 (m-30) cc_final: 0.6695 (m-30) REVERT: G 13 HIS cc_start: 0.3944 (OUTLIER) cc_final: 0.3447 (m-70) REVERT: J 23 ASP cc_start: 0.7420 (m-30) cc_final: 0.7147 (m-30) REVERT: I 13 HIS cc_start: 0.4620 (OUTLIER) cc_final: 0.4205 (m170) REVERT: I 16 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6769 (ptmm) REVERT: I 17 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6713 (pp) outliers start: 28 outliers final: 12 residues processed: 71 average time/residue: 0.8480 time to fit residues: 61.8769 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 : 0.230 ------------------------------------------------------------------------------- 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 16 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2110 Z= 0.259 Angle : 0.687 7.123 2830 Z= 0.327 Chirality : 0.057 0.129 330 Planarity : 0.003 0.017 360 Dihedral : 7.378 43.244 293 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 13.81 % Allowed : 15.71 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.44), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 14 PHE 0.014 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 85 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.239 Fit side-chains REVERT: D 13 HIS cc_start: 0.4585 (OUTLIER) cc_final: 0.4253 (m-70) REVERT: C 13 HIS cc_start: 0.3755 (OUTLIER) cc_final: 0.3532 (m-70) REVERT: C 15 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: E 15 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: E 26 SER cc_start: 0.8338 (p) cc_final: 0.8044 (p) REVERT: B 13 HIS cc_start: 0.4941 (OUTLIER) cc_final: 0.3980 (t70) REVERT: B 23 ASP cc_start: 0.7738 (m-30) cc_final: 0.7499 (m-30) REVERT: A 13 HIS cc_start: 0.4334 (OUTLIER) cc_final: 0.3899 (m-70) REVERT: A 15 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7334 (OUTLIER) REVERT: A 34 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7550 (mp) REVERT: H 23 ASP cc_start: 0.7045 (m-30) cc_final: 0.6700 (m-30) REVERT: J 23 ASP cc_start: 0.7468 (m-30) cc_final: 0.7181 (m-30) REVERT: I 17 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6654 (pp) outliers start: 29 outliers final: 13 residues processed: 70 average time/residue: 0.6485 time to fit residues: 46.9175 Evaluate side-chains 75 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 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 9 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 0.0170 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.8424 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2110 Z= 0.391 Angle : 0.816 8.737 2830 Z= 0.373 Chirality : 0.062 0.137 330 Planarity : 0.003 0.014 360 Dihedral : 8.256 53.228 293 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 14.76 % Allowed : 13.81 % 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 (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: -3.15 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 14 PHE 0.019 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 86 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.228 Fit side-chains REVERT: D 13 HIS cc_start: 0.4568 (OUTLIER) cc_final: 0.4169 (m-70) REVERT: C 13 HIS cc_start: 0.3996 (OUTLIER) cc_final: 0.3547 (m-70) REVERT: C 15 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: E 13 HIS cc_start: 0.3887 (OUTLIER) cc_final: 0.3581 (m170) REVERT: E 15 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: E 26 SER cc_start: 0.8214 (p) cc_final: 0.7909 (p) REVERT: B 13 HIS cc_start: 0.4943 (OUTLIER) cc_final: 0.4024 (t70) REVERT: B 23 ASP cc_start: 0.7709 (m-30) cc_final: 0.7462 (m-30) REVERT: A 13 HIS cc_start: 0.4322 (OUTLIER) cc_final: 0.3891 (m90) REVERT: A 34 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7462 (mp) REVERT: H 23 ASP cc_start: 0.7094 (m-30) cc_final: 0.6812 (m-30) REVERT: J 23 ASP cc_start: 0.7402 (m-30) cc_final: 0.7165 (m-30) REVERT: I 17 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6615 (pp) outliers start: 31 outliers final: 18 residues processed: 68 average time/residue: 0.6432 time to fit residues: 45.3652 Evaluate side-chains 79 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2998 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= 0.355 Angle : 0.799 8.598 2830 Z= 0.364 Chirality : 0.060 0.133 330 Planarity : 0.003 0.014 360 Dihedral : 8.139 51.694 293 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 16.67 % Allowed : 17.14 % Favored : 66.19 % 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 : -2.42 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.017 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 90 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.244 Fit side-chains REVERT: D 13 HIS cc_start: 0.4373 (OUTLIER) cc_final: 0.4045 (m-70) REVERT: C 13 HIS cc_start: 0.3919 (OUTLIER) cc_final: 0.3485 (m-70) REVERT: E 13 HIS cc_start: 0.3939 (OUTLIER) cc_final: 0.3689 (m170) REVERT: E 15 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: B 13 HIS cc_start: 0.4917 (OUTLIER) cc_final: 0.4023 (t70) REVERT: A 13 HIS cc_start: 0.4244 (OUTLIER) cc_final: 0.3882 (m-70) REVERT: A 34 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7467 (mp) REVERT: H 23 ASP cc_start: 0.7137 (m-30) cc_final: 0.6860 (m-30) REVERT: I 13 HIS cc_start: 0.4521 (OUTLIER) cc_final: 0.4126 (m170) REVERT: I 17 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6626 (pp) outliers start: 35 outliers final: 20 residues processed: 71 average time/residue: 0.6359 time to fit residues: 46.6837 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 : 0.226 ------------------------------------------------------------------------------- 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 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 15 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 overall best weight: 6.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 2110 Z= 0.630 Angle : 1.029 11.658 2830 Z= 0.466 Chirality : 0.072 0.208 330 Planarity : 0.004 0.016 360 Dihedral : 9.027 57.358 293 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.78 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: -3.35 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 14 PHE 0.024 0.004 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 87 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.232 Fit side-chains REVERT: D 13 HIS cc_start: 0.4437 (OUTLIER) cc_final: 0.4048 (m-70) REVERT: C 13 HIS cc_start: 0.4003 (OUTLIER) cc_final: 0.3448 (m170) REVERT: E 13 HIS cc_start: 0.4229 (OUTLIER) cc_final: 0.3857 (m170) REVERT: E 15 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: B 13 HIS cc_start: 0.4949 (OUTLIER) cc_final: 0.4105 (t70) REVERT: B 23 ASP cc_start: 0.7741 (m-30) cc_final: 0.7536 (m-30) REVERT: A 13 HIS cc_start: 0.4307 (OUTLIER) cc_final: 0.3788 (m-70) REVERT: I 13 HIS cc_start: 0.4609 (OUTLIER) cc_final: 0.4195 (m90) REVERT: I 17 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6620 (pp) outliers start: 33 outliers final: 21 residues processed: 72 average time/residue: 0.7211 time to fit residues: 53.5100 Evaluate side-chains 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 15 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2110 Z= 0.209 Angle : 0.679 8.791 2830 Z= 0.314 Chirality : 0.056 0.128 330 Planarity : 0.002 0.011 360 Dihedral : 7.062 38.406 293 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 11.43 % Allowed : 20.48 % 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: -3.29 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 14 PHE 0.015 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 82 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.245 Fit side-chains REVERT: D 13 HIS cc_start: 0.4152 (OUTLIER) cc_final: 0.3895 (m-70) REVERT: C 13 HIS cc_start: 0.3822 (OUTLIER) cc_final: 0.3342 (m90) REVERT: B 13 HIS cc_start: 0.4862 (OUTLIER) cc_final: 0.3963 (t70) REVERT: I 17 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6612 (pp) REVERT: I 19 PHE cc_start: 0.7407 (t80) cc_final: 0.7090 (t80) outliers start: 24 outliers final: 14 residues processed: 68 average time/residue: 0.7183 time to fit residues: 50.3935 Evaluate side-chains 72 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 B residue 13 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL 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 14 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2110 Z= 0.456 Angle : 0.898 11.250 2830 Z= 0.409 Chirality : 0.064 0.172 330 Planarity : 0.003 0.020 360 Dihedral : 8.460 49.212 292 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 12.38 % Allowed : 19.52 % 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: -3.34 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 14 PHE 0.021 0.004 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 82 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.204 Fit side-chains REVERT: D 13 HIS cc_start: 0.4348 (OUTLIER) cc_final: 0.4005 (m-70) REVERT: C 13 HIS cc_start: 0.4016 (OUTLIER) cc_final: 0.3453 (m90) REVERT: B 13 HIS cc_start: 0.4954 (OUTLIER) cc_final: 0.4122 (t70) REVERT: B 23 ASP cc_start: 0.7724 (m-30) cc_final: 0.7512 (m-30) REVERT: A 13 HIS cc_start: 0.4504 (OUTLIER) cc_final: 0.4098 (m-70) REVERT: A 34 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7781 (tt) REVERT: I 17 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6651 (pp) outliers start: 26 outliers final: 17 residues processed: 68 average time/residue: 0.7301 time to fit residues: 51.1402 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 : 0.245 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2110 Z= 0.335 Angle : 0.791 10.730 2830 Z= 0.362 Chirality : 0.059 0.132 330 Planarity : 0.003 0.018 360 Dihedral : 8.079 47.843 292 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 12.86 % Allowed : 19.52 % 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: -3.30 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.016 0.003 PHE C 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 84 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.228 Fit side-chains REVERT: D 13 HIS cc_start: 0.4245 (OUTLIER) cc_final: 0.3959 (m-70) REVERT: C 13 HIS cc_start: 0.3994 (OUTLIER) cc_final: 0.3420 (m90) REVERT: B 13 HIS cc_start: 0.4999 (OUTLIER) cc_final: 0.4165 (t70) REVERT: B 23 ASP cc_start: 0.7731 (m-30) cc_final: 0.7523 (m-30) REVERT: A 13 HIS cc_start: 0.4517 (OUTLIER) cc_final: 0.3904 (m-70) REVERT: A 34 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7750 (tt) REVERT: I 17 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6616 (pp) outliers start: 27 outliers final: 17 residues processed: 69 average time/residue: 0.6768 time to fit residues: 48.1851 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 : 0.228 ------------------------------------------------------------------------------- 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 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 B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS 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 J residue 40 VAL 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 18 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2110 Z= 0.187 Angle : 0.641 9.885 2830 Z= 0.301 Chirality : 0.054 0.133 330 Planarity : 0.002 0.012 360 Dihedral : 6.857 36.853 292 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 : 10.48 % Allowed : 21.90 % 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: -3.21 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 14 PHE 0.016 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 76 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.231 Fit side-chains REVERT: D 13 HIS cc_start: 0.3992 (OUTLIER) cc_final: 0.3748 (m-70) REVERT: E 26 SER cc_start: 0.8259 (p) cc_final: 0.7950 (p) REVERT: B 13 HIS cc_start: 0.4975 (OUTLIER) cc_final: 0.4138 (t70) REVERT: A 13 HIS cc_start: 0.4411 (OUTLIER) cc_final: 0.3906 (m-70) REVERT: A 17 LEU cc_start: 0.7360 (pt) cc_final: 0.6844 (mp) REVERT: I 17 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6586 (pp) REVERT: I 19 PHE cc_start: 0.7420 (t80) cc_final: 0.7070 (t80) outliers start: 22 outliers final: 15 residues processed: 66 average time/residue: 0.7681 time to fit residues: 52.2360 Evaluate side-chains 71 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 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 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 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 B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 VAL 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 16 optimal weight: 0.0030 chunk 18 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8014 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.161521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106479 restraints weight = 1700.545| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.34 r_work: 0.3338 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2110 Z= 0.140 Angle : 0.582 9.474 2830 Z= 0.277 Chirality : 0.053 0.129 330 Planarity : 0.002 0.014 360 Dihedral : 6.171 31.134 292 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 7.14 % Allowed : 25.71 % 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: -3.15 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 14 PHE 0.019 0.002 PHE A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.52 seconds wall clock time: 30 minutes 35.36 seconds (1835.36 seconds total)