Starting phenix.real_space_refine on Fri Aug 22 13:31:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot4_17168/08_2025/8ot4_17168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot4_17168/08_2025/8ot4_17168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ot4_17168/08_2025/8ot4_17168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot4_17168/08_2025/8ot4_17168.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot4_17168/08_2025/8ot4_17168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot4_17168/08_2025/8ot4_17168.cif" } resolution = 2.97 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= 0.002 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 12 5.16 5 C 2184 2.51 5 N 600 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.48, per 1000 atoms: 0.14 Number of scatterers: 3444 At special positions: 0 Unit cell: (75.92, 80.08, 49.92, 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 12 16.00 O 648 8.00 N 600 7.00 C 2184 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: 0.26 Conformation dependent library (CDL) restraints added in 130.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.588A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 11 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU I 11 " --> pdb=" O VAL K 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 24 removed outlier: 6.562A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA K 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE I 20 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP K 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU I 22 " --> pdb=" O ASP K 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.589A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU J 11 " --> pdb=" O VAL L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.563A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA L 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE J 20 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP L 23 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU J 22 " --> pdb=" O ASP L 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 No hydrogen bonds 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: 0.02 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 800 1.33 - 1.45: 808 1.45 - 1.56: 1884 1.56 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 3516 Sorted by residual: bond pdb=" N VAL K 36 " pdb=" CA VAL K 36 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.42e+00 bond pdb=" N VAL G 36 " pdb=" CA VAL G 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.31e+00 bond pdb=" N VAL I 36 " pdb=" CA VAL I 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N VAL J 36 " pdb=" CA VAL J 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.21e+00 bond pdb=" N VAL D 36 " pdb=" CA VAL D 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.20e+00 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 3163 2.06 - 4.11: 1219 4.11 - 6.17: 250 6.17 - 8.23: 48 8.23 - 10.29: 24 Bond angle restraints: 4704 Sorted by residual: angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 112.04 101.75 10.29 1.44e+00 4.82e-01 5.10e+01 angle pdb=" N GLU L 22 " pdb=" CA GLU L 22 " pdb=" C GLU L 22 " ideal model delta sigma weight residual 112.04 101.77 10.27 1.44e+00 4.82e-01 5.09e+01 angle pdb=" N GLU J 22 " pdb=" CA GLU J 22 " pdb=" C GLU J 22 " ideal model delta sigma weight residual 112.04 101.77 10.27 1.44e+00 4.82e-01 5.09e+01 angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 112.04 101.78 10.26 1.44e+00 4.82e-01 5.08e+01 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 112.04 101.78 10.26 1.44e+00 4.82e-01 5.08e+01 ... (remaining 4699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.93: 1560 10.93 - 21.86: 240 21.86 - 32.78: 132 32.78 - 43.71: 12 43.71 - 54.64: 36 Dihedral angle restraints: 1980 sinusoidal: 768 harmonic: 1212 Sorted by residual: dihedral pdb=" CA ILE E 31 " pdb=" CB ILE E 31 " pdb=" CG1 ILE E 31 " pdb=" CD1 ILE E 31 " ideal model delta sinusoidal sigma weight residual 60.00 109.27 -49.27 3 1.50e+01 4.44e-03 8.75e+00 dihedral pdb=" CA ILE C 31 " pdb=" CB ILE C 31 " pdb=" CG1 ILE C 31 " pdb=" CD1 ILE C 31 " ideal model delta sinusoidal sigma weight residual 60.00 109.27 -49.27 3 1.50e+01 4.44e-03 8.75e+00 dihedral pdb=" CA ILE F 31 " pdb=" CB ILE F 31 " pdb=" CG1 ILE F 31 " pdb=" CD1 ILE F 31 " ideal model delta sinusoidal sigma weight residual 60.00 109.26 -49.26 3 1.50e+01 4.44e-03 8.75e+00 ... (remaining 1977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 74 0.056 - 0.112: 186 0.112 - 0.168: 135 0.168 - 0.224: 73 0.224 - 0.280: 12 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA ILE G 31 " pdb=" N ILE G 31 " pdb=" C ILE G 31 " pdb=" CB ILE G 31 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 477 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 31 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ILE I 31 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE I 31 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE I 32 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 31 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ILE K 31 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE K 31 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE K 32 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 31 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ILE E 31 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE E 31 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE E 32 " -0.024 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 1668 3.00 - 3.48: 3051 3.48 - 3.95: 5775 3.95 - 4.43: 6610 4.43 - 4.90: 12473 Nonbonded interactions: 29577 Sorted by model distance: nonbonded pdb=" N HIS E 13 " pdb=" O HIS E 13 " model vdw 2.527 2.496 nonbonded pdb=" N HIS I 13 " pdb=" O HIS I 13 " model vdw 2.528 2.496 nonbonded pdb=" N HIS C 13 " pdb=" O HIS C 13 " model vdw 2.528 2.496 nonbonded pdb=" N HIS F 13 " pdb=" O HIS F 13 " model vdw 2.528 2.496 nonbonded pdb=" N HIS H 13 " pdb=" O HIS H 13 " model vdw 2.528 2.496 ... (remaining 29572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.500 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.860 Find NCS groups from input model: 0.010 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.012 0.036 3516 Z= 0.892 Angle : 2.301 10.287 4704 Z= 1.670 Chirality : 0.127 0.280 480 Planarity : 0.014 0.039 624 Dihedral : 15.194 54.635 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 5 TYR 0.005 0.002 TYR C 10 PHE 0.012 0.003 PHE I 4 HIS 0.005 0.002 HIS A 6 Details of bonding type rmsd covalent geometry : bond 0.01186 ( 3516) covalent geometry : angle 2.30127 ( 4704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 TYR cc_start: 0.7942 (t80) cc_final: 0.5771 (p90) REVERT: L 5 ARG cc_start: 0.7697 (mtp180) cc_final: 0.6688 (tpt170) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5619 time to fit residues: 74.9259 Evaluate side-chains 109 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS F 15 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS ** K 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS L 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.242755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.206981 restraints weight = 4670.985| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 1.69 r_work: 0.4199 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3516 Z= 0.122 Angle : 0.617 4.993 4704 Z= 0.327 Chirality : 0.050 0.126 480 Planarity : 0.002 0.011 624 Dihedral : 5.432 13.942 456 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.16 % Allowed : 24.71 % Favored : 72.13 % 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: -2.85 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 5 TYR 0.011 0.001 TYR I 10 PHE 0.014 0.003 PHE G 20 HIS 0.012 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3516) covalent geometry : angle 0.61679 ( 4704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.135 Fit side-chains REVERT: A 13 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6640 (m90) REVERT: C 3 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: C 11 GLU cc_start: 0.7366 (tt0) cc_final: 0.6625 (tt0) REVERT: C 28 LYS cc_start: 0.8554 (tttt) cc_final: 0.8344 (ttmt) REVERT: D 28 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8409 (tmtp) REVERT: E 28 LYS cc_start: 0.8487 (tmtp) cc_final: 0.7979 (ttmt) REVERT: F 3 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: G 3 GLU cc_start: 0.7660 (tt0) cc_final: 0.6997 (tm-30) REVERT: H 13 HIS cc_start: 0.6364 (OUTLIER) cc_final: 0.6163 (m90) REVERT: H 28 LYS cc_start: 0.8564 (tmtp) cc_final: 0.8185 (tttt) REVERT: I 15 GLN cc_start: 0.8341 (tt0) cc_final: 0.7773 (tt0) REVERT: I 28 LYS cc_start: 0.8682 (tmtp) cc_final: 0.8169 (ttmt) REVERT: J 3 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: J 28 LYS cc_start: 0.8686 (tmmm) cc_final: 0.8176 (ttpt) outliers start: 11 outliers final: 1 residues processed: 90 average time/residue: 0.6471 time to fit residues: 59.6630 Evaluate side-chains 86 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN ** K 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.238147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.202845 restraints weight = 4680.416| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 1.58 r_work: 0.4907 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.4819 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3516 Z= 0.131 Angle : 0.593 4.502 4704 Z= 0.314 Chirality : 0.050 0.128 480 Planarity : 0.002 0.012 624 Dihedral : 5.272 14.939 456 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.16 % Allowed : 26.72 % Favored : 70.11 % 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: -2.65 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 5 TYR 0.003 0.000 TYR D 10 PHE 0.018 0.003 PHE F 19 HIS 0.006 0.001 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3516) covalent geometry : angle 0.59301 ( 4704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.141 Fit side-chains REVERT: B 13 HIS cc_start: 0.6292 (m-70) cc_final: 0.5575 (m-70) REVERT: D 10 TYR cc_start: 0.7638 (t80) cc_final: 0.7435 (t80) REVERT: G 28 LYS cc_start: 0.8227 (tmtp) cc_final: 0.7894 (tttt) REVERT: J 28 LYS cc_start: 0.8396 (tmmm) cc_final: 0.8164 (ttpt) REVERT: L 5 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7267 (tpt170) outliers start: 11 outliers final: 3 residues processed: 86 average time/residue: 0.7295 time to fit residues: 64.1165 Evaluate side-chains 80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain L residue 13 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.233419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.195396 restraints weight = 4723.231| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 1.56 r_work: 0.4143 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3516 Z= 0.232 Angle : 0.690 4.317 4704 Z= 0.373 Chirality : 0.051 0.132 480 Planarity : 0.002 0.012 624 Dihedral : 5.734 18.164 456 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.16 % Allowed : 26.15 % Favored : 70.69 % 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: -2.60 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 5 TYR 0.006 0.001 TYR B 10 PHE 0.022 0.004 PHE G 4 HIS 0.007 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 3516) covalent geometry : angle 0.68999 ( 4704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.141 Fit side-chains REVERT: A 11 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7580 (mt-10) REVERT: B 5 ARG cc_start: 0.8485 (mtp180) cc_final: 0.7029 (ttp-170) REVERT: B 10 TYR cc_start: 0.8641 (t80) cc_final: 0.5374 (p90) REVERT: B 13 HIS cc_start: 0.6783 (m-70) cc_final: 0.6014 (m-70) REVERT: D 11 GLU cc_start: 0.7682 (tt0) cc_final: 0.7296 (tt0) REVERT: D 28 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8116 (ttmt) REVERT: F 3 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7086 (tm-30) REVERT: F 13 HIS cc_start: 0.6670 (m-70) cc_final: 0.6155 (m90) REVERT: H 28 LYS cc_start: 0.8442 (tmtp) cc_final: 0.8058 (ttmt) REVERT: J 1 ASP cc_start: 0.7160 (p0) cc_final: 0.6725 (m-30) REVERT: J 3 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6902 (tm-30) REVERT: J 11 GLU cc_start: 0.7691 (tt0) cc_final: 0.6809 (tt0) REVERT: J 28 LYS cc_start: 0.8651 (tmmm) cc_final: 0.8263 (ttpt) REVERT: L 5 ARG cc_start: 0.8236 (mtp180) cc_final: 0.6798 (tpt170) outliers start: 11 outliers final: 4 residues processed: 85 average time/residue: 0.7268 time to fit residues: 63.1412 Evaluate side-chains 80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain L residue 13 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 13 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 HIS ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS I 13 HIS ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 HIS L 13 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.120099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.100821 restraints weight = 5492.467| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.03 r_work: 0.3877 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 3516 Z= 0.378 Angle : 0.812 5.503 4704 Z= 0.447 Chirality : 0.053 0.129 480 Planarity : 0.003 0.012 624 Dihedral : 6.295 20.349 456 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.02 % Allowed : 27.30 % Favored : 68.68 % 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: -2.83 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 5 TYR 0.011 0.001 TYR K 10 PHE 0.026 0.005 PHE C 4 HIS 0.007 0.001 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00828 ( 3516) covalent geometry : angle 0.81190 ( 4704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.092 Fit side-chains REVERT: A 11 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 28 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5055 (tppt) REVERT: B 11 GLU cc_start: 0.7815 (tt0) cc_final: 0.7141 (tt0) REVERT: D 28 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7977 (ttmt) REVERT: F 3 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6860 (tm-30) REVERT: J 1 ASP cc_start: 0.7056 (p0) cc_final: 0.6397 (m-30) REVERT: J 3 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6758 (tm-30) REVERT: J 28 LYS cc_start: 0.8691 (tmmm) cc_final: 0.8292 (ttpt) REVERT: K 5 ARG cc_start: 0.8137 (mtp180) cc_final: 0.6429 (mmt-90) REVERT: L 5 ARG cc_start: 0.8239 (mtp180) cc_final: 0.6721 (tpt170) outliers start: 14 outliers final: 4 residues processed: 83 average time/residue: 0.7802 time to fit residues: 66.0529 Evaluate side-chains 81 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain L residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.229324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.191965 restraints weight = 4824.746| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.45 r_work: 0.4064 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3516 Z= 0.204 Angle : 0.692 7.812 4704 Z= 0.370 Chirality : 0.052 0.129 480 Planarity : 0.002 0.010 624 Dihedral : 5.920 18.972 456 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.02 % Allowed : 27.87 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 5 TYR 0.005 0.001 TYR D 10 PHE 0.016 0.003 PHE C 4 HIS 0.006 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3516) covalent geometry : angle 0.69224 ( 4704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.137 Fit side-chains REVERT: A 11 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 3 GLU cc_start: 0.7810 (tm-30) cc_final: 0.6884 (tm-30) REVERT: C 5 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7963 (mtp180) REVERT: C 35 MET cc_start: 0.7906 (ttm) cc_final: 0.7689 (ttm) REVERT: D 28 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8117 (ttmt) REVERT: F 3 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6934 (tm-30) REVERT: H 11 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7773 (tt0) REVERT: H 28 LYS cc_start: 0.8309 (tmtp) cc_final: 0.7805 (ttmt) REVERT: J 3 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6986 (tm-30) REVERT: J 28 LYS cc_start: 0.8711 (tmmm) cc_final: 0.8329 (ttpt) REVERT: K 5 ARG cc_start: 0.8099 (mtp180) cc_final: 0.6623 (mmt-90) REVERT: L 5 ARG cc_start: 0.8199 (mtp180) cc_final: 0.6783 (tpt170) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.7908 time to fit residues: 61.3742 Evaluate side-chains 79 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.230538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.192084 restraints weight = 4898.166| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.62 r_work: 0.4056 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3516 Z= 0.191 Angle : 0.660 7.377 4704 Z= 0.354 Chirality : 0.051 0.129 480 Planarity : 0.002 0.012 624 Dihedral : 5.827 18.162 456 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.17 % Allowed : 28.74 % Favored : 66.09 % 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: -2.68 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 5 TYR 0.012 0.001 TYR K 10 PHE 0.017 0.003 PHE C 4 HIS 0.005 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 3516) covalent geometry : angle 0.66004 ( 4704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.087 Fit side-chains REVERT: A 11 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 28 LYS cc_start: 0.5953 (OUTLIER) cc_final: 0.4487 (tppt) REVERT: B 13 HIS cc_start: 0.6745 (m-70) cc_final: 0.5835 (m-70) REVERT: C 3 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: C 5 ARG cc_start: 0.8277 (mtp180) cc_final: 0.8059 (mtp180) REVERT: D 28 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8076 (ttmt) REVERT: F 3 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6921 (tm-30) REVERT: H 11 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7744 (tt0) REVERT: H 28 LYS cc_start: 0.8321 (tmtp) cc_final: 0.7840 (ttmt) REVERT: J 3 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6955 (tm-30) REVERT: J 13 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6934 (m90) REVERT: J 28 LYS cc_start: 0.8721 (tmmm) cc_final: 0.8367 (ttpt) REVERT: K 5 ARG cc_start: 0.8137 (mtp180) cc_final: 0.6632 (mmt-90) REVERT: L 5 ARG cc_start: 0.8207 (mtp180) cc_final: 0.6770 (tpt170) outliers start: 18 outliers final: 6 residues processed: 75 average time/residue: 0.7775 time to fit residues: 59.4797 Evaluate side-chains 80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain L residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 HIS K 15 GLN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.234909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.197096 restraints weight = 4813.692| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.62 r_work: 0.4108 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3516 Z= 0.144 Angle : 0.612 6.702 4704 Z= 0.327 Chirality : 0.051 0.127 480 Planarity : 0.002 0.012 624 Dihedral : 5.505 16.174 456 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.16 % Allowed : 31.03 % Favored : 65.80 % 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: -2.56 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.004 0.001 TYR F 10 PHE 0.013 0.002 PHE G 4 HIS 0.005 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3516) covalent geometry : angle 0.61179 ( 4704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.141 Fit side-chains REVERT: A 11 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7401 (mt-10) REVERT: B 11 GLU cc_start: 0.7531 (tt0) cc_final: 0.7245 (tt0) REVERT: B 13 HIS cc_start: 0.6288 (m-70) cc_final: 0.5910 (m-70) REVERT: C 3 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: C 5 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7916 (ttt90) REVERT: D 28 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8039 (ttmt) REVERT: F 3 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6958 (tm-30) REVERT: G 3 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7230 (tm-30) REVERT: G 28 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7992 (ttmt) REVERT: H 11 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8115 (mt-10) REVERT: H 28 LYS cc_start: 0.8312 (tmtp) cc_final: 0.7838 (ttmt) REVERT: J 3 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7025 (tm-30) REVERT: J 28 LYS cc_start: 0.8676 (tmmm) cc_final: 0.8314 (ttpt) REVERT: L 5 ARG cc_start: 0.8166 (mtp180) cc_final: 0.6794 (tpt170) outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 0.7515 time to fit residues: 59.1624 Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.235107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.197335 restraints weight = 4664.229| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 1.63 r_work: 0.4942 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.4859 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.4859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3516 Z= 0.137 Angle : 0.607 6.295 4704 Z= 0.325 Chirality : 0.051 0.127 480 Planarity : 0.002 0.011 624 Dihedral : 5.323 15.697 456 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.45 % Allowed : 31.61 % Favored : 64.94 % 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: -2.46 (0.37), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 5 TYR 0.015 0.001 TYR K 10 PHE 0.011 0.002 PHE C 4 HIS 0.004 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3516) covalent geometry : angle 0.60703 ( 4704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.139 Fit side-chains REVERT: C 1 ASP cc_start: 0.6907 (p0) cc_final: 0.6639 (m-30) REVERT: I 13 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5944 (m-70) REVERT: J 28 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8147 (ttpt) REVERT: L 5 ARG cc_start: 0.7889 (mtp180) cc_final: 0.7464 (tpt170) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 0.7077 time to fit residues: 54.2936 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.230763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.191449 restraints weight = 4803.194| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.63 r_work: 0.4071 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3516 Z= 0.230 Angle : 0.725 7.416 4704 Z= 0.392 Chirality : 0.052 0.129 480 Planarity : 0.002 0.014 624 Dihedral : 5.644 17.215 456 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.30 % Allowed : 34.20 % Favored : 63.51 % 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: -2.59 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 5 TYR 0.006 0.001 TYR B 10 PHE 0.023 0.003 PHE C 4 HIS 0.007 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 3516) covalent geometry : angle 0.72487 ( 4704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.143 Fit side-chains REVERT: A 11 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7549 (tt0) REVERT: C 3 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7334 (tm-30) REVERT: I 13 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.5884 (m-70) REVERT: J 28 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8352 (ttpt) REVERT: K 5 ARG cc_start: 0.8122 (mtp180) cc_final: 0.6630 (tpt170) REVERT: L 5 ARG cc_start: 0.8222 (mtp180) cc_final: 0.6839 (tpt170) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.7848 time to fit residues: 53.7132 Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.234044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.195278 restraints weight = 4802.117| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.68 r_work: 0.4111 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3516 Z= 0.163 Angle : 0.688 6.728 4704 Z= 0.368 Chirality : 0.052 0.128 480 Planarity : 0.002 0.018 624 Dihedral : 5.556 18.506 456 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 35.63 % Favored : 62.07 % 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 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 5 TYR 0.014 0.001 TYR K 10 PHE 0.015 0.002 PHE C 4 HIS 0.005 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3516) covalent geometry : angle 0.68820 ( 4704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.99 seconds wall clock time: 28 minutes 28.70 seconds (1708.70 seconds total)