Starting phenix.real_space_refine on Fri Oct 10 10:17:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf3_37197/10_2025/8kf3_37197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf3_37197/10_2025/8kf3_37197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kf3_37197/10_2025/8kf3_37197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf3_37197/10_2025/8kf3_37197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kf3_37197/10_2025/8kf3_37197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf3_37197/10_2025/8kf3_37197.map" } resolution = 3.5 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= 0.001 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 9 5.16 5 C 1419 2.51 5 N 369 2.21 5 O 378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 0.97, per 1000 atoms: 0.45 Number of scatterers: 2175 At special positions: 0 Unit cell: (63.91, 95.45, 39.84, 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 9 16.00 O 378 8.00 N 369 7.00 C 1419 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: 0.22 Conformation dependent library (CDL) restraints added in 84.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AA3, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.609A pdb=" N ILE D 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET E 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE E 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N MET F 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 18 removed outlier: 9.112A pdb=" N GLU H 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N HIS G 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS H 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LYS G 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN H 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL G 18 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU H 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL I 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 30 through 35 removed outlier: 6.250A pdb=" N ILE H 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU G 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY H 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU I 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY G 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 15 removed outlier: 6.377A pdb=" N TYR B 10 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS A 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 12 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A 15 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS B 14 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS C 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN C 15 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N HIS A 14 " --> pdb=" O GLN C 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.173A pdb=" N ILE B 31 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 41 20 hydrogen bonds defined for protein. 60 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: 0.27 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 705 1.34 - 1.45: 294 1.45 - 1.57: 1191 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 2208 Sorted by residual: bond pdb=" CB LYS C 16 " pdb=" CG LYS C 16 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" N GLY G 29 " pdb=" CA GLY G 29 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.23e+00 bond pdb=" CB LYS A 16 " pdb=" CG LYS A 16 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CG GLN G 15 " pdb=" CD GLN G 15 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB LYS B 16 " pdb=" CG LYS B 16 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 2203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 2668 1.34 - 2.68: 243 2.68 - 4.02: 38 4.02 - 5.36: 13 5.36 - 6.70: 2 Bond angle restraints: 2964 Sorted by residual: angle pdb=" N ASP G 23 " pdb=" CA ASP G 23 " pdb=" CB ASP G 23 " ideal model delta sigma weight residual 114.17 109.99 4.18 1.14e+00 7.69e-01 1.34e+01 angle pdb=" C GLU C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N VAL E 36 " pdb=" CA VAL E 36 " pdb=" C VAL E 36 " ideal model delta sigma weight residual 111.62 108.89 2.73 7.90e-01 1.60e+00 1.20e+01 angle pdb=" N ASP H 23 " pdb=" CA ASP H 23 " pdb=" CB ASP H 23 " ideal model delta sigma weight residual 114.17 110.44 3.73 1.14e+00 7.69e-01 1.07e+01 angle pdb=" C GLU A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 ... (remaining 2959 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.76: 1015 11.76 - 23.52: 139 23.52 - 35.28: 51 35.28 - 47.03: 21 47.03 - 58.79: 4 Dihedral angle restraints: 1230 sinusoidal: 444 harmonic: 786 Sorted by residual: dihedral pdb=" CA ASP C 23 " pdb=" C ASP C 23 " pdb=" N VAL C 24 " pdb=" CA VAL C 24 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 23 " pdb=" C ASP A 23 " pdb=" N VAL A 24 " pdb=" CA VAL A 24 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP B 23 " pdb=" C ASP B 23 " pdb=" N VAL B 24 " pdb=" CA VAL B 24 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 124 0.027 - 0.053: 86 0.053 - 0.080: 48 0.080 - 0.107: 47 0.107 - 0.133: 40 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA HIS H 14 " pdb=" N HIS H 14 " pdb=" C HIS H 14 " pdb=" CB HIS H 14 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL I 12 " pdb=" N VAL I 12 " pdb=" C VAL I 12 " pdb=" CB VAL I 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 342 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 23 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ASP H 23 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP H 23 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL H 24 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 22 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C GLU I 22 " 0.018 2.00e-02 2.50e+03 pdb=" O GLU I 22 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP I 23 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 23 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.77e-01 pdb=" C ASP G 23 " 0.015 2.00e-02 2.50e+03 pdb=" O ASP G 23 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL G 24 " -0.005 2.00e-02 2.50e+03 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 722 2.88 - 3.39: 1695 3.39 - 3.89: 3635 3.89 - 4.40: 3687 4.40 - 4.90: 7218 Nonbonded interactions: 16957 Sorted by model distance: nonbonded pdb=" O VAL D 12 " pdb=" N VAL E 12 " model vdw 2.379 3.120 nonbonded pdb=" OE2 GLU H 22 " pdb=" NZ LYS G 16 " model vdw 2.573 3.120 nonbonded pdb=" ND2 ASN C 27 " pdb=" O GLY C 29 " model vdw 2.588 3.120 nonbonded pdb=" ND2 ASN A 27 " pdb=" O GLY A 29 " model vdw 2.590 3.120 nonbonded pdb=" O VAL E 12 " pdb=" N VAL F 12 " model vdw 2.604 3.120 ... (remaining 16952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 42) selection = (chain 'B' and resid 12 through 42) selection = (chain 'C' and resid 12 through 42) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 12 through 42) selection = (chain 'H' and resid 12 through 42) selection = (chain 'I' and resid 12 through 42) } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.940 Find NCS groups from input model: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.008 0.034 2208 Z= 0.359 Angle : 0.862 6.696 2964 Z= 0.502 Chirality : 0.063 0.133 345 Planarity : 0.003 0.011 372 Dihedral : 13.984 58.791 738 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: -3.58 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 10 PHE 0.009 0.002 PHE C 20 HIS 0.006 0.002 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00791 ( 2208) covalent geometry : angle 0.86183 ( 2964) hydrogen bonds : bond 0.14788 ( 20) hydrogen bonds : angle 7.93745 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0624 time to fit residues: 2.1353 Evaluate side-chains 22 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 27 ASN H 13 HIS E 27 ASN G 13 HIS F 15 GLN F 27 ASN I 13 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095577 restraints weight = 2336.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096744 restraints weight = 1925.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097338 restraints weight = 1717.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098017 restraints weight = 1621.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098017 restraints weight = 1535.145| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2208 Z= 0.142 Angle : 0.594 5.531 2964 Z= 0.321 Chirality : 0.058 0.140 345 Planarity : 0.002 0.015 372 Dihedral : 4.612 12.769 294 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.37 % Allowed : 9.13 % Favored : 89.50 % 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: -2.99 (0.44), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR G 10 PHE 0.005 0.001 PHE C 20 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2208) covalent geometry : angle 0.59422 ( 2964) hydrogen bonds : bond 0.03004 ( 20) hydrogen bonds : angle 5.69352 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.097 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.0612 time to fit residues: 2.0230 Evaluate side-chains 23 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105038 restraints weight = 2244.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106935 restraints weight = 1739.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108287 restraints weight = 1482.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109013 restraints weight = 1340.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109013 restraints weight = 1255.109| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 2208 Z= 0.071 Angle : 0.463 4.726 2964 Z= 0.253 Chirality : 0.057 0.133 345 Planarity : 0.002 0.011 372 Dihedral : 3.899 12.153 294 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.83 % Allowed : 13.24 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.46), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 10 PHE 0.005 0.001 PHE D 19 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00140 ( 2208) covalent geometry : angle 0.46296 ( 2964) hydrogen bonds : bond 0.02083 ( 20) hydrogen bonds : angle 4.75754 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.134 Fit side-chains REVERT: E 34 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8276 (tt) REVERT: G 28 LYS cc_start: 0.8456 (mttt) cc_final: 0.8017 (mtpp) outliers start: 4 outliers final: 0 residues processed: 27 average time/residue: 0.0661 time to fit residues: 2.2088 Evaluate side-chains 24 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101812 restraints weight = 2301.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102367 restraints weight = 2011.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103148 restraints weight = 1879.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103148 restraints weight = 1749.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103148 restraints weight = 1749.857| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2208 Z= 0.239 Angle : 0.659 7.360 2964 Z= 0.354 Chirality : 0.060 0.132 345 Planarity : 0.002 0.013 372 Dihedral : 4.372 12.460 294 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.74 % Allowed : 13.24 % Favored : 84.02 % 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: -2.55 (0.47), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR G 10 PHE 0.007 0.002 PHE E 20 HIS 0.005 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 2208) covalent geometry : angle 0.65932 ( 2964) hydrogen bonds : bond 0.02867 ( 20) hydrogen bonds : angle 5.02810 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.100 Fit side-chains REVERT: E 34 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8296 (tt) REVERT: F 34 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8338 (tt) outliers start: 6 outliers final: 2 residues processed: 27 average time/residue: 0.0649 time to fit residues: 2.1245 Evaluate side-chains 26 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 35 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.125483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095253 restraints weight = 2299.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096691 restraints weight = 1839.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097776 restraints weight = 1609.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098277 restraints weight = 1474.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098277 restraints weight = 1405.296| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2208 Z= 0.154 Angle : 0.585 6.682 2964 Z= 0.315 Chirality : 0.058 0.129 345 Planarity : 0.002 0.012 372 Dihedral : 4.182 11.437 294 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 1.83 % Allowed : 14.16 % Favored : 84.02 % 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: -2.42 (0.48), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR G 10 PHE 0.005 0.001 PHE E 20 HIS 0.004 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2208) covalent geometry : angle 0.58532 ( 2964) hydrogen bonds : bond 0.02519 ( 20) hydrogen bonds : angle 4.89387 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.080 Fit side-chains REVERT: E 34 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (tt) REVERT: F 34 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8316 (tt) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.0604 time to fit residues: 1.9378 Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 35 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.2980 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.126154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096279 restraints weight = 2274.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097540 restraints weight = 1890.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098493 restraints weight = 1683.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098817 restraints weight = 1552.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098817 restraints weight = 1502.012| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2208 Z= 0.116 Angle : 0.527 5.696 2964 Z= 0.286 Chirality : 0.058 0.127 345 Planarity : 0.002 0.012 372 Dihedral : 3.913 11.556 294 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.83 % Allowed : 14.61 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.48), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR G 10 PHE 0.005 0.001 PHE F 20 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 2208) covalent geometry : angle 0.52669 ( 2964) hydrogen bonds : bond 0.02210 ( 20) hydrogen bonds : angle 4.75751 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.091 Fit side-chains REVERT: E 34 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8208 (tt) REVERT: F 34 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8320 (tt) REVERT: F 35 MET cc_start: 0.8303 (tpt) cc_final: 0.8041 (tpt) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.0592 time to fit residues: 2.0495 Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.132227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102384 restraints weight = 2267.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103958 restraints weight = 1839.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105132 restraints weight = 1610.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105617 restraints weight = 1475.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105639 restraints weight = 1409.723| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2208 Z= 0.074 Angle : 0.460 5.252 2964 Z= 0.250 Chirality : 0.057 0.131 345 Planarity : 0.002 0.010 372 Dihedral : 3.576 11.588 294 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.37 % Allowed : 15.53 % Favored : 83.11 % 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: -2.15 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 10 PHE 0.005 0.001 PHE D 19 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00151 ( 2208) covalent geometry : angle 0.46037 ( 2964) hydrogen bonds : bond 0.01825 ( 20) hydrogen bonds : angle 4.52698 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: E 34 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8233 (tt) REVERT: F 34 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8305 (tt) REVERT: F 35 MET cc_start: 0.8306 (tpt) cc_final: 0.7972 (tpt) outliers start: 3 outliers final: 0 residues processed: 28 average time/residue: 0.0621 time to fit residues: 2.1437 Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.129030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096234 restraints weight = 2117.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096275 restraints weight = 1705.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096275 restraints weight = 1683.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096275 restraints weight = 1683.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096275 restraints weight = 1682.978| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2208 Z= 0.182 Angle : 0.585 5.132 2964 Z= 0.320 Chirality : 0.059 0.133 345 Planarity : 0.002 0.012 372 Dihedral : 4.047 12.079 294 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.28 % Allowed : 15.98 % Favored : 81.74 % 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: -2.25 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 10 PHE 0.007 0.001 PHE D 19 HIS 0.005 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 2208) covalent geometry : angle 0.58509 ( 2964) hydrogen bonds : bond 0.02556 ( 20) hydrogen bonds : angle 4.82181 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.069 Fit side-chains REVERT: D 34 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8296 (tt) REVERT: E 34 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8262 (tt) REVERT: F 34 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8288 (tt) outliers start: 5 outliers final: 0 residues processed: 28 average time/residue: 0.0578 time to fit residues: 1.9670 Evaluate side-chains 26 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.123704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093353 restraints weight = 2242.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094636 restraints weight = 1849.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095524 restraints weight = 1631.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095766 restraints weight = 1510.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095766 restraints weight = 1470.503| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2208 Z= 0.121 Angle : 0.524 4.987 2964 Z= 0.286 Chirality : 0.058 0.129 345 Planarity : 0.002 0.012 372 Dihedral : 3.880 11.360 294 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.28 % Allowed : 15.53 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.15 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR G 10 PHE 0.007 0.001 PHE D 19 HIS 0.003 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2208) covalent geometry : angle 0.52399 ( 2964) hydrogen bonds : bond 0.02272 ( 20) hydrogen bonds : angle 4.76447 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.087 Fit side-chains REVERT: D 34 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8290 (tt) REVERT: E 34 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8246 (tt) REVERT: F 34 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8305 (tt) outliers start: 5 outliers final: 0 residues processed: 32 average time/residue: 0.0542 time to fit residues: 2.1345 Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3764 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.121099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.090669 restraints weight = 2270.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.091850 restraints weight = 1886.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092712 restraints weight = 1677.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092712 restraints weight = 1549.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092712 restraints weight = 1549.313| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2208 Z= 0.170 Angle : 0.580 4.915 2964 Z= 0.318 Chirality : 0.058 0.132 345 Planarity : 0.002 0.012 372 Dihedral : 4.022 11.736 294 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.37 % Allowed : 15.98 % Favored : 82.65 % 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: -2.21 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR G 10 PHE 0.006 0.001 PHE E 20 HIS 0.004 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2208) covalent geometry : angle 0.57965 ( 2964) hydrogen bonds : bond 0.02522 ( 20) hydrogen bonds : angle 4.83954 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.051 Fit side-chains REVERT: D 34 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8284 (tt) REVERT: E 34 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8231 (tt) REVERT: F 34 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8307 (tt) outliers start: 3 outliers final: 0 residues processed: 28 average time/residue: 0.0562 time to fit residues: 1.9079 Evaluate side-chains 26 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 overall best weight: 1.4258 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.125792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095176 restraints weight = 2286.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096533 restraints weight = 1844.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097501 restraints weight = 1620.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097726 restraints weight = 1493.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098419 restraints weight = 1450.939| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2208 Z= 0.111 Angle : 0.519 4.853 2964 Z= 0.284 Chirality : 0.057 0.130 345 Planarity : 0.002 0.012 372 Dihedral : 3.822 11.448 294 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.37 % Allowed : 16.89 % Favored : 81.74 % 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: -2.15 (0.49), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR G 10 PHE 0.005 0.001 PHE F 20 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 2208) covalent geometry : angle 0.51933 ( 2964) hydrogen bonds : bond 0.02179 ( 20) hydrogen bonds : angle 4.72801 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 660.01 seconds wall clock time: 11 minutes 58.29 seconds (718.29 seconds total)