Starting phenix.real_space_refine on Tue Mar 3 10:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykw_33897/03_2026/7ykw_33897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykw_33897/03_2026/7ykw_33897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_2026/7ykw_33897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_2026/7ykw_33897.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_2026/7ykw_33897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_2026/7ykw_33897.cif" } resolution = 3.6 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= 0.003 sd= 0.040 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 8 5.16 5 C 1164 2.51 5 N 356 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "H" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 0.49, per 1000 atoms: 0.26 Number of scatterers: 1908 At special positions: 0 Unit cell: (86.32, 86.32, 37.44, 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 8 16.00 O 380 8.00 N 356 7.00 C 1164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 7 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 42.1 milliseconds 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 62.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.569A pdb=" N ASN A 35 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN C 35 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN E 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 22 removed outlier: 6.585A pdb=" N THR B 6 " --> pdb=" O CYS D 7 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N THR D 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 8 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ARG D 11 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN B 10 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA D 13 " --> pdb=" O GLN B 10 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 12 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE D 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN B 14 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL D 17 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 16 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER D 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS B 18 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ASN D 21 " --> pdb=" O HIS B 18 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER B 20 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR F 6 " --> pdb=" O CYS H 7 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR H 9 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA F 8 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ARG H 11 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN F 10 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA H 13 " --> pdb=" O GLN F 10 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU F 12 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE H 15 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN F 14 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL H 17 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU F 16 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER H 19 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N HIS F 18 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN H 21 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER F 20 " --> pdb=" O ASN H 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 32 removed outlier: 6.405A pdb=" N ILE B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N SER D 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 28 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASN D 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N THR B 30 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 26 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER F 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 28 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN F 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR D 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE F 26 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER H 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER F 28 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASN H 31 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR F 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.579A pdb=" N ASN B 35 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN D 35 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN F 35 " --> pdb=" O THR H 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 61 hydrogen bonds defined for protein. 183 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: 0.26 Time building geometry restraints manager: 0.18 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: 636 1.33 - 1.45: 405 1.45 - 1.57: 883 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 1932 Sorted by residual: bond pdb=" C THR D 36 " pdb=" N TYC D 37 " ideal model delta sigma weight residual 1.329 1.261 0.068 1.40e-02 5.10e+03 2.33e+01 bond pdb=" C THR B 36 " pdb=" N TYC B 37 " ideal model delta sigma weight residual 1.329 1.262 0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" C THR F 36 " pdb=" N TYC F 37 " ideal model delta sigma weight residual 1.329 1.263 0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" C THR H 36 " pdb=" N TYC H 37 " ideal model delta sigma weight residual 1.329 1.263 0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C THR G 36 " pdb=" N TYC G 37 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.40e-02 5.10e+03 9.62e+00 ... (remaining 1927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 2143 1.69 - 3.38: 299 3.38 - 5.07: 136 5.07 - 6.76: 25 6.76 - 8.45: 21 Bond angle restraints: 2624 Sorted by residual: angle pdb=" N ALA D 5 " pdb=" CA ALA D 5 " pdb=" C ALA D 5 " ideal model delta sigma weight residual 111.36 104.26 7.10 1.09e+00 8.42e-01 4.24e+01 angle pdb=" N ALA F 5 " pdb=" CA ALA F 5 " pdb=" C ALA F 5 " ideal model delta sigma weight residual 111.28 105.14 6.14 1.09e+00 8.42e-01 3.17e+01 angle pdb=" N PHE F 23 " pdb=" CA PHE F 23 " pdb=" C PHE F 23 " ideal model delta sigma weight residual 108.49 100.04 8.45 1.65e+00 3.67e-01 2.62e+01 angle pdb=" N PHE B 23 " pdb=" CA PHE B 23 " pdb=" C PHE B 23 " ideal model delta sigma weight residual 108.49 100.06 8.43 1.65e+00 3.67e-01 2.61e+01 angle pdb=" N PHE D 23 " pdb=" CA PHE D 23 " pdb=" C PHE D 23 " ideal model delta sigma weight residual 108.49 100.07 8.42 1.65e+00 3.67e-01 2.60e+01 ... (remaining 2619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 1040 13.40 - 26.80: 68 26.80 - 40.20: 33 40.20 - 53.60: 12 53.60 - 67.00: 3 Dihedral angle restraints: 1156 sinusoidal: 428 harmonic: 728 Sorted by residual: dihedral pdb=" CB CYS D 2 " pdb=" SG CYS D 2 " pdb=" SG CYS D 7 " pdb=" CB CYS D 7 " ideal model delta sinusoidal sigma weight residual -86.00 -153.00 67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -142.11 56.11 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS H 2 " pdb=" SG CYS H 2 " pdb=" SG CYS H 7 " pdb=" CB CYS H 7 " ideal model delta sinusoidal sigma weight residual -86.00 -141.48 55.48 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 1153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 150 0.047 - 0.095: 83 0.095 - 0.142: 43 0.142 - 0.189: 24 0.189 - 0.236: 16 Chirality restraints: 316 Sorted by residual: chirality pdb=" CA PHE F 23 " pdb=" N PHE F 23 " pdb=" C PHE F 23 " pdb=" CB PHE F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE B 23 " pdb=" N PHE B 23 " pdb=" C PHE B 23 " pdb=" CB PHE B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE D 23 " pdb=" N PHE D 23 " pdb=" C PHE D 23 " pdb=" CB PHE D 23 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 313 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 36 " -0.017 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C THR A 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC A 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 36 " -0.017 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C THR C 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC C 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " -0.017 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C THR E 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1213 3.01 - 3.48: 1824 3.48 - 3.96: 3224 3.96 - 4.43: 3548 4.43 - 4.90: 6479 Nonbonded interactions: 16288 Sorted by model distance: nonbonded pdb=" N ASN F 3 " pdb=" N THR F 4 " model vdw 2.538 2.560 nonbonded pdb=" N ASN B 3 " pdb=" N THR B 4 " model vdw 2.547 2.560 nonbonded pdb=" C THR B 4 " pdb=" OG1 THR B 4 " model vdw 2.561 2.616 nonbonded pdb=" N ASN D 3 " pdb=" N THR D 4 " model vdw 2.567 2.560 nonbonded pdb=" N ASN B 3 " pdb=" O CYS D 2 " model vdw 2.568 3.120 ... (remaining 16283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.010 0.068 1936 Z= 0.725 Angle : 1.662 8.448 2632 Z= 1.047 Chirality : 0.088 0.236 316 Planarity : 0.004 0.031 344 Dihedral : 11.456 44.566 664 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % 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 are not related in a simple way. whole: -3.01 (0.43), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 11 PHE 0.011 0.002 PHE E 23 HIS 0.001 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00960 ( 1932) covalent geometry : angle 1.66268 ( 2624) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.39462 ( 8) hydrogen bonds : bond 0.10258 ( 61) hydrogen bonds : angle 8.61047 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.074 Fit side-chains REVERT: A 23 PHE cc_start: 0.8129 (m-80) cc_final: 0.6485 (p90) REVERT: B 15 PHE cc_start: 0.7833 (m-80) cc_final: 0.6294 (p90) REVERT: D 14 ASN cc_start: 0.7680 (m-40) cc_final: 0.7330 (m-40) REVERT: F 14 ASN cc_start: 0.7757 (m-40) cc_final: 0.7386 (m-40) REVERT: G 22 ASN cc_start: 0.8296 (t0) cc_final: 0.7862 (t0) REVERT: G 35 ASN cc_start: 0.8321 (m-40) cc_final: 0.8078 (m-40) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0253 time to fit residues: 3.2660 Evaluate side-chains 52 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 31 ASN B 14 ASN B 21 ASN B 31 ASN C 21 ASN C 31 ASN D 21 ASN D 31 ASN E 21 ASN E 31 ASN F 21 ASN F 31 ASN G 21 ASN G 31 ASN H 21 ASN H 31 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.096002 restraints weight = 5196.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.098251 restraints weight = 2202.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.099561 restraints weight = 1311.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.100123 restraints weight = 997.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.100191 restraints weight = 884.701| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1936 Z= 0.164 Angle : 0.624 9.221 2632 Z= 0.303 Chirality : 0.041 0.114 316 Planarity : 0.002 0.013 344 Dihedral : 5.568 20.178 312 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.88 % Allowed : 17.31 % Favored : 79.81 % 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 are not related in a simple way. whole: -3.63 (0.40), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.31), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 PHE 0.012 0.001 PHE D 15 HIS 0.002 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 1932) covalent geometry : angle 0.61678 ( 2624) SS BOND : bond 0.00160 ( 4) SS BOND : angle 1.77935 ( 8) hydrogen bonds : bond 0.02464 ( 61) hydrogen bonds : angle 5.79979 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.073 Fit side-chains REVERT: B 16 LEU cc_start: 0.7913 (tp) cc_final: 0.7506 (tp) REVERT: D 14 ASN cc_start: 0.7692 (m-40) cc_final: 0.7383 (m-40) REVERT: F 14 ASN cc_start: 0.7625 (m-40) cc_final: 0.7262 (m-40) REVERT: G 22 ASN cc_start: 0.8269 (t0) cc_final: 0.8049 (t0) REVERT: H 22 ASN cc_start: 0.8003 (t0) cc_final: 0.6388 (p0) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0210 time to fit residues: 1.9851 Evaluate side-chains 53 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 40.0000 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN F 18 HIS F 22 ASN H 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.103532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.083413 restraints weight = 5230.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.085117 restraints weight = 2227.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.085994 restraints weight = 1376.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.086209 restraints weight = 1096.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.086789 restraints weight = 1027.838| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 1936 Z= 0.426 Angle : 0.703 8.860 2632 Z= 0.363 Chirality : 0.043 0.153 316 Planarity : 0.003 0.016 344 Dihedral : 8.531 26.106 312 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.88 % Allowed : 18.27 % Favored : 78.85 % 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 are not related in a simple way. whole: -3.90 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 11 PHE 0.016 0.002 PHE B 15 HIS 0.004 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00862 ( 1932) covalent geometry : angle 0.69929 ( 2624) SS BOND : bond 0.00181 ( 4) SS BOND : angle 1.51258 ( 8) hydrogen bonds : bond 0.02715 ( 61) hydrogen bonds : angle 5.32194 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.043 Fit side-chains REVERT: D 14 ASN cc_start: 0.8085 (m-40) cc_final: 0.7483 (m-40) REVERT: F 14 ASN cc_start: 0.7870 (m-40) cc_final: 0.7555 (p0) REVERT: F 16 LEU cc_start: 0.9046 (tp) cc_final: 0.8820 (tp) REVERT: G 15 PHE cc_start: 0.8057 (t80) cc_final: 0.7661 (t80) REVERT: G 22 ASN cc_start: 0.8548 (t0) cc_final: 0.8340 (t0) REVERT: G 27 LEU cc_start: 0.8935 (tt) cc_final: 0.8717 (tt) REVERT: H 16 LEU cc_start: 0.8183 (tp) cc_final: 0.7499 (pt) REVERT: H 22 ASN cc_start: 0.8150 (t0) cc_final: 0.6972 (p0) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.0221 time to fit residues: 1.7147 Evaluate side-chains 50 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.127656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.092460 restraints weight = 5189.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.094715 restraints weight = 2161.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.095999 restraints weight = 1324.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.096885 restraints weight = 1043.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.097223 restraints weight = 900.951| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1936 Z= 0.204 Angle : 0.548 6.219 2632 Z= 0.278 Chirality : 0.038 0.120 316 Planarity : 0.002 0.013 344 Dihedral : 5.691 17.955 312 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.40 % Allowed : 20.67 % Favored : 76.92 % 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 are not related in a simple way. whole: -4.10 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 PHE 0.009 0.001 PHE F 15 HIS 0.002 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 1932) covalent geometry : angle 0.54451 ( 2624) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.26729 ( 8) hydrogen bonds : bond 0.01900 ( 61) hydrogen bonds : angle 4.82929 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.052 Fit side-chains REVERT: A 15 PHE cc_start: 0.3349 (p90) cc_final: 0.3043 (p90) REVERT: D 14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7473 (m-40) REVERT: F 14 ASN cc_start: 0.7835 (m-40) cc_final: 0.7423 (p0) REVERT: F 16 LEU cc_start: 0.9031 (tp) cc_final: 0.8731 (tp) REVERT: G 27 LEU cc_start: 0.8832 (tt) cc_final: 0.8392 (tt) REVERT: H 16 LEU cc_start: 0.8114 (tp) cc_final: 0.7242 (pt) REVERT: H 17 VAL cc_start: 0.9293 (t) cc_final: 0.9059 (p) REVERT: H 22 ASN cc_start: 0.7959 (t0) cc_final: 0.6783 (p0) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.0216 time to fit residues: 1.6019 Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN D 18 HIS G 35 ASN H 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.097635 restraints weight = 5209.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.100019 restraints weight = 2190.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.101489 restraints weight = 1338.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.102323 restraints weight = 1030.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.102587 restraints weight = 887.239| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1936 Z= 0.120 Angle : 0.544 9.295 2632 Z= 0.262 Chirality : 0.039 0.113 316 Planarity : 0.002 0.013 344 Dihedral : 4.726 16.856 312 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.92 % Allowed : 22.12 % Favored : 75.96 % 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 are not related in a simple way. whole: -4.21 (0.40), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 PHE 0.005 0.001 PHE F 15 HIS 0.001 0.000 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1932) covalent geometry : angle 0.54121 ( 2624) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.11119 ( 8) hydrogen bonds : bond 0.01853 ( 61) hydrogen bonds : angle 4.58215 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.082 Fit side-chains REVERT: B 14 ASN cc_start: 0.5031 (OUTLIER) cc_final: 0.4434 (t0) REVERT: D 14 ASN cc_start: 0.7835 (m-40) cc_final: 0.7483 (m-40) REVERT: E 30 THR cc_start: 0.9624 (m) cc_final: 0.9188 (p) REVERT: F 14 ASN cc_start: 0.7798 (m-40) cc_final: 0.7436 (p0) REVERT: F 16 LEU cc_start: 0.9093 (tp) cc_final: 0.8886 (tp) REVERT: G 22 ASN cc_start: 0.7997 (t0) cc_final: 0.6498 (p0) REVERT: H 16 LEU cc_start: 0.8098 (tp) cc_final: 0.7235 (pt) REVERT: H 22 ASN cc_start: 0.7866 (t0) cc_final: 0.6775 (p0) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.0224 time to fit residues: 1.6354 Evaluate side-chains 47 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN H 3 ASN H 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.101327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.080161 restraints weight = 5269.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.081857 restraints weight = 2324.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.082887 restraints weight = 1495.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.083385 restraints weight = 1180.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.083481 restraints weight = 1050.369| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 1936 Z= 0.500 Angle : 0.719 8.155 2632 Z= 0.380 Chirality : 0.043 0.179 316 Planarity : 0.003 0.024 344 Dihedral : 8.707 37.497 312 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.40 % Allowed : 21.63 % Favored : 75.96 % 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 are not related in a simple way. whole: -4.34 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 11 PHE 0.020 0.003 PHE B 15 HIS 0.007 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.01012 ( 1932) covalent geometry : angle 0.71765 ( 2624) SS BOND : bond 0.00167 ( 4) SS BOND : angle 1.03536 ( 8) hydrogen bonds : bond 0.02261 ( 61) hydrogen bonds : angle 4.99234 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.073 Fit side-chains REVERT: F 14 ASN cc_start: 0.7749 (m-40) cc_final: 0.7435 (p0) REVERT: H 22 ASN cc_start: 0.8242 (t0) cc_final: 0.7131 (p0) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.0249 time to fit residues: 1.5261 Evaluate side-chains 44 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.0000 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.133001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.096129 restraints weight = 5090.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.098418 restraints weight = 2213.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.099606 restraints weight = 1357.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.099606 restraints weight = 1061.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.099607 restraints weight = 1061.612| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1936 Z= 0.124 Angle : 0.529 7.521 2632 Z= 0.259 Chirality : 0.039 0.119 316 Planarity : 0.002 0.011 344 Dihedral : 5.239 25.643 312 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.44 % Allowed : 22.12 % Favored : 76.44 % 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 are not related in a simple way. whole: -4.40 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 11 PHE 0.010 0.001 PHE D 15 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 1932) covalent geometry : angle 0.52652 ( 2624) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.99878 ( 8) hydrogen bonds : bond 0.02255 ( 61) hydrogen bonds : angle 4.59563 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.070 Fit side-chains REVERT: B 16 LEU cc_start: 0.7489 (tp) cc_final: 0.7202 (tp) REVERT: D 14 ASN cc_start: 0.8173 (m-40) cc_final: 0.7602 (t0) REVERT: E 30 THR cc_start: 0.9619 (m) cc_final: 0.9204 (p) REVERT: G 22 ASN cc_start: 0.7252 (t0) cc_final: 0.5785 (p0) REVERT: H 16 LEU cc_start: 0.7704 (tp) cc_final: 0.6891 (pt) REVERT: H 22 ASN cc_start: 0.8152 (t0) cc_final: 0.6899 (p0) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.0226 time to fit residues: 1.5913 Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 ASN F 14 ASN H 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.107996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.086722 restraints weight = 4975.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088662 restraints weight = 2138.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.089758 restraints weight = 1311.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.090369 restraints weight = 1019.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.090544 restraints weight = 898.666| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1936 Z= 0.230 Angle : 0.555 7.472 2632 Z= 0.279 Chirality : 0.039 0.137 316 Planarity : 0.002 0.011 344 Dihedral : 6.037 30.260 312 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.44 % Allowed : 23.08 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 11 PHE 0.008 0.001 PHE B 15 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 1932) covalent geometry : angle 0.55334 ( 2624) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.92508 ( 8) hydrogen bonds : bond 0.02090 ( 61) hydrogen bonds : angle 4.61749 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.044 Fit side-chains REVERT: D 14 ASN cc_start: 0.7726 (m-40) cc_final: 0.7166 (p0) REVERT: E 30 THR cc_start: 0.9667 (m) cc_final: 0.9239 (p) REVERT: H 16 LEU cc_start: 0.7826 (tp) cc_final: 0.7000 (pt) REVERT: H 22 ASN cc_start: 0.7318 (t0) cc_final: 0.6494 (p0) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.0215 time to fit residues: 1.4216 Evaluate side-chains 47 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.133008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.094898 restraints weight = 5219.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.097199 restraints weight = 2273.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.098380 restraints weight = 1416.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.099314 restraints weight = 1130.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.099489 restraints weight = 978.927| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1936 Z= 0.157 Angle : 0.542 7.920 2632 Z= 0.264 Chirality : 0.039 0.129 316 Planarity : 0.002 0.010 344 Dihedral : 5.380 29.301 312 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.44 % Allowed : 23.08 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 11 PHE 0.007 0.001 PHE B 15 HIS 0.001 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1932) covalent geometry : angle 0.54036 ( 2624) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.94703 ( 8) hydrogen bonds : bond 0.02021 ( 61) hydrogen bonds : angle 4.59909 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.074 Fit side-chains REVERT: D 14 ASN cc_start: 0.7838 (m-40) cc_final: 0.7047 (p0) REVERT: E 30 THR cc_start: 0.9643 (m) cc_final: 0.9242 (p) REVERT: G 27 LEU cc_start: 0.8446 (tp) cc_final: 0.8204 (tt) REVERT: H 16 LEU cc_start: 0.7679 (tp) cc_final: 0.6891 (pt) REVERT: H 22 ASN cc_start: 0.7342 (t0) cc_final: 0.6465 (p0) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.0239 time to fit residues: 1.5717 Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.106230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.084709 restraints weight = 5000.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.086535 restraints weight = 2224.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.087603 restraints weight = 1397.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.088033 restraints weight = 1083.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.088033 restraints weight = 981.464| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 1936 Z= 0.312 Angle : 0.605 7.655 2632 Z= 0.305 Chirality : 0.040 0.138 316 Planarity : 0.002 0.012 344 Dihedral : 6.844 38.825 312 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.92 % Allowed : 22.60 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 11 PHE 0.011 0.002 PHE B 15 HIS 0.002 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00634 ( 1932) covalent geometry : angle 0.60365 ( 2624) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.93169 ( 8) hydrogen bonds : bond 0.02042 ( 61) hydrogen bonds : angle 4.77748 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.068 Fit side-chains REVERT: D 14 ASN cc_start: 0.7987 (m-40) cc_final: 0.7544 (p0) REVERT: H 16 LEU cc_start: 0.7971 (tp) cc_final: 0.7030 (pt) REVERT: H 22 ASN cc_start: 0.7556 (t0) cc_final: 0.6548 (p0) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.0214 time to fit residues: 1.4132 Evaluate side-chains 46 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.111604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.090516 restraints weight = 4907.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.092483 restraints weight = 2152.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.093718 restraints weight = 1305.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.094429 restraints weight = 986.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.094725 restraints weight = 846.271| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1936 Z= 0.121 Angle : 0.538 8.226 2632 Z= 0.258 Chirality : 0.040 0.138 316 Planarity : 0.002 0.009 344 Dihedral : 5.291 30.768 312 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.48 % Allowed : 25.00 % Favored : 74.52 % 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 are not related in a simple way. whole: -4.45 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 11 PHE 0.007 0.001 PHE D 15 HIS 0.001 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 1932) covalent geometry : angle 0.53605 ( 2624) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.92277 ( 8) hydrogen bonds : bond 0.02130 ( 61) hydrogen bonds : angle 4.68861 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 546.25 seconds wall clock time: 10 minutes 20.50 seconds (620.50 seconds total)