Starting phenix.real_space_refine on Wed Jul 23 07:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykw_33897/07_2025/7ykw_33897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykw_33897/07_2025/7ykw_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_33897/07_2025/7ykw_33897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykw_33897/07_2025/7ykw_33897.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykw_33897/07_2025/7ykw_33897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykw_33897/07_2025/7ykw_33897.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.20, per 1000 atoms: 1.15 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: 0.69 Conformation dependent library (CDL) restraints added in 232.7 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: 0.35 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: 0.55 Time building geometry restraints manager: 0.58 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.980 Find NCS groups from input model: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (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 HIS 0.001 0.001 HIS G 18 PHE 0.011 0.002 PHE E 23 ARG 0.002 0.001 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.10258 ( 61) hydrogen bonds : angle 8.61047 ( 183) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.39462 ( 8) covalent geometry : bond 0.00960 ( 1932) covalent geometry : angle 1.66268 ( 2624) *********************** 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 : 0.232 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: 0.0654 time to fit residues: 8.1935 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 : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.126573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.102303 restraints weight = 4962.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.104542 restraints weight = 1986.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.105766 restraints weight = 1144.474| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1936 Z= 0.177 Angle : 0.632 9.272 2632 Z= 0.308 Chirality : 0.040 0.113 316 Planarity : 0.002 0.012 344 Dihedral : 5.618 20.796 312 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.88 % Allowed : 17.79 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.41), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.31), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.010 0.001 PHE D 15 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02557 ( 61) hydrogen bonds : angle 5.83677 ( 183) SS BOND : bond 0.00156 ( 4) SS BOND : angle 1.77837 ( 8) covalent geometry : bond 0.00334 ( 1932) covalent geometry : angle 0.62492 ( 2624) *********************** 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 : 0.233 Fit side-chains revert: symmetry clash REVERT: F 14 ASN cc_start: 0.7701 (m-40) cc_final: 0.7397 (t0) REVERT: H 22 ASN cc_start: 0.8317 (t0) cc_final: 0.6811 (p0) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.0673 time to fit residues: 6.1835 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 : 0.230 ------------------------------------------------------------------------------- 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 10 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.124597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.091011 restraints weight = 5294.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.093142 restraints weight = 2251.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094475 restraints weight = 1415.771| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1936 Z= 0.293 Angle : 0.624 8.999 2632 Z= 0.317 Chirality : 0.041 0.121 316 Planarity : 0.003 0.014 344 Dihedral : 6.495 18.137 312 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.92 % Allowed : 19.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.40), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.012 0.002 PHE B 15 ARG 0.001 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.02467 ( 61) hydrogen bonds : angle 5.07601 ( 183) SS BOND : bond 0.00180 ( 4) SS BOND : angle 1.54113 ( 8) covalent geometry : bond 0.00587 ( 1932) covalent geometry : angle 0.61958 ( 2624) *********************** 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 56 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.242 Fit side-chains REVERT: F 14 ASN cc_start: 0.8034 (m-40) cc_final: 0.7353 (p0) REVERT: H 16 LEU cc_start: 0.8313 (tp) cc_final: 0.7551 (pt) REVERT: H 22 ASN cc_start: 0.8073 (t0) cc_final: 0.6865 (p0) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.0709 time to fit residues: 5.0340 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL 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 17 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 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 = 0.4175 r_free = 0.4175 target = 0.107481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.087640 restraints weight = 4933.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.089497 restraints weight = 2081.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.090349 restraints weight = 1259.823| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1936 Z= 0.261 Angle : 0.543 5.963 2632 Z= 0.285 Chirality : 0.039 0.118 316 Planarity : 0.002 0.014 344 Dihedral : 6.196 18.467 312 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.88 % Allowed : 18.75 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.011 0.002 PHE D 15 ARG 0.001 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.02014 ( 61) hydrogen bonds : angle 4.76980 ( 183) SS BOND : bond 0.00156 ( 4) SS BOND : angle 1.22778 ( 8) covalent geometry : bond 0.00516 ( 1932) covalent geometry : angle 0.53948 ( 2624) *********************** 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 52 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.213 Fit side-chains REVERT: B 16 LEU cc_start: 0.6958 (tp) cc_final: 0.6701 (tp) REVERT: E 30 THR cc_start: 0.9653 (m) cc_final: 0.9279 (p) REVERT: F 14 ASN cc_start: 0.8008 (m-40) cc_final: 0.7508 (p0) REVERT: H 16 LEU cc_start: 0.8315 (tp) cc_final: 0.7492 (pt) REVERT: H 22 ASN cc_start: 0.8035 (t0) cc_final: 0.6865 (p0) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.0626 time to fit residues: 4.2796 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR 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 11 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 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 = 0.4247 r_free = 0.4247 target = 0.117509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.094275 restraints weight = 4934.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.096602 restraints weight = 1973.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.097939 restraints weight = 1166.634| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1936 Z= 0.136 Angle : 0.523 9.430 2632 Z= 0.257 Chirality : 0.039 0.116 316 Planarity : 0.002 0.016 344 Dihedral : 4.855 16.982 312 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.92 % Allowed : 20.67 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.006 0.001 PHE G 23 ARG 0.001 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.01946 ( 61) hydrogen bonds : angle 4.48888 ( 183) SS BOND : bond 0.00181 ( 4) SS BOND : angle 1.07804 ( 8) covalent geometry : bond 0.00271 ( 1932) covalent geometry : angle 0.52059 ( 2624) *********************** 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 56 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.261 Fit side-chains REVERT: E 30 THR cc_start: 0.9628 (m) cc_final: 0.9274 (p) REVERT: F 14 ASN cc_start: 0.7786 (m-40) cc_final: 0.7468 (p0) REVERT: H 16 LEU cc_start: 0.8185 (tp) cc_final: 0.7314 (pt) REVERT: H 22 ASN cc_start: 0.7854 (t0) cc_final: 0.6717 (p0) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.0719 time to fit residues: 5.2190 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.109851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.089259 restraints weight = 4939.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.091330 restraints weight = 2075.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.092584 restraints weight = 1257.975| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5738 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= 0.180 Angle : 0.520 6.750 2632 Z= 0.261 Chirality : 0.039 0.113 316 Planarity : 0.002 0.011 344 Dihedral : 5.238 20.146 312 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.96 % Allowed : 22.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.39), 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 HIS 0.002 0.000 HIS H 18 PHE 0.010 0.001 PHE B 15 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.01887 ( 61) hydrogen bonds : angle 4.40257 ( 183) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.95689 ( 8) covalent geometry : bond 0.00359 ( 1932) covalent geometry : angle 0.51791 ( 2624) *********************** 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: 2 poor density : 44 time to evaluate : 0.262 Fit side-chains REVERT: A 23 PHE cc_start: 0.9183 (m-80) cc_final: 0.7009 (p90) REVERT: E 30 THR cc_start: 0.9652 (m) cc_final: 0.9283 (p) REVERT: F 14 ASN cc_start: 0.7729 (m-40) cc_final: 0.7385 (p0) REVERT: H 16 LEU cc_start: 0.8246 (tp) cc_final: 0.7434 (pt) REVERT: H 22 ASN cc_start: 0.7942 (t0) cc_final: 0.6807 (p0) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.0799 time to fit residues: 4.7619 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.126902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.091366 restraints weight = 5214.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.093502 restraints weight = 2246.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.094832 restraints weight = 1395.000| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1936 Z= 0.298 Angle : 0.621 8.783 2632 Z= 0.305 Chirality : 0.039 0.118 316 Planarity : 0.002 0.015 344 Dihedral : 6.575 29.020 312 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.013 0.002 PHE B 15 ARG 0.001 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.01943 ( 61) hydrogen bonds : angle 4.53242 ( 183) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.91297 ( 8) covalent geometry : bond 0.00599 ( 1932) covalent geometry : angle 0.61964 ( 2624) *********************** 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 49 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.209 Fit side-chains REVERT: E 30 THR cc_start: 0.9653 (m) cc_final: 0.9239 (p) REVERT: F 14 ASN cc_start: 0.7617 (m-40) cc_final: 0.7317 (p0) REVERT: H 16 LEU cc_start: 0.8333 (tp) cc_final: 0.7467 (pt) REVERT: H 22 ASN cc_start: 0.8292 (t0) cc_final: 0.7151 (p0) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.0631 time to fit residues: 4.0939 Evaluate side-chains 46 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.093768 restraints weight = 5295.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.096156 restraints weight = 2240.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.097542 restraints weight = 1361.083| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1936 Z= 0.173 Angle : 0.548 7.588 2632 Z= 0.265 Chirality : 0.039 0.126 316 Planarity : 0.002 0.012 344 Dihedral : 5.297 27.599 312 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.009 0.001 PHE B 15 ARG 0.001 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.01918 ( 61) hydrogen bonds : angle 4.44227 ( 183) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.94749 ( 8) covalent geometry : bond 0.00349 ( 1932) covalent geometry : angle 0.54626 ( 2624) *********************** 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 47 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.242 Fit side-chains REVERT: E 27 LEU cc_start: 0.8902 (tp) cc_final: 0.8422 (mp) REVERT: E 30 THR cc_start: 0.9643 (m) cc_final: 0.9280 (p) REVERT: H 16 LEU cc_start: 0.8216 (tp) cc_final: 0.7310 (pt) REVERT: H 22 ASN cc_start: 0.8101 (t0) cc_final: 0.6836 (p0) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.0672 time to fit residues: 4.2686 Evaluate side-chains 43 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.118323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.093452 restraints weight = 5252.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.095779 restraints weight = 2253.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.096925 restraints weight = 1368.996| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1936 Z= 0.141 Angle : 0.544 7.907 2632 Z= 0.261 Chirality : 0.039 0.139 316 Planarity : 0.002 0.011 344 Dihedral : 5.035 26.378 312 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.44 % Allowed : 21.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 18 PHE 0.007 0.001 PHE B 15 ARG 0.000 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.01901 ( 61) hydrogen bonds : angle 4.35453 ( 183) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.90467 ( 8) covalent geometry : bond 0.00287 ( 1932) covalent geometry : angle 0.54283 ( 2624) *********************** 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 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.241 Fit side-chains REVERT: E 27 LEU cc_start: 0.9065 (tp) cc_final: 0.8538 (mp) REVERT: E 30 THR cc_start: 0.9658 (m) cc_final: 0.9285 (p) REVERT: H 16 LEU cc_start: 0.8121 (tp) cc_final: 0.7163 (pt) REVERT: H 22 ASN cc_start: 0.6715 (t0) cc_final: 0.5920 (p0) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.0665 time to fit residues: 4.2342 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.108187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.087266 restraints weight = 4988.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.089217 restraints weight = 2134.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.090372 restraints weight = 1293.617| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 1936 Z= 0.242 Angle : 0.603 7.784 2632 Z= 0.290 Chirality : 0.039 0.162 316 Planarity : 0.002 0.012 344 Dihedral : 6.017 32.451 312 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.44 % Allowed : 21.15 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.011 0.001 PHE B 15 ARG 0.001 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.01941 ( 61) hydrogen bonds : angle 4.45624 ( 183) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.89339 ( 8) covalent geometry : bond 0.00491 ( 1932) covalent geometry : angle 0.60161 ( 2624) ********************** 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 44 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.236 Fit side-chains REVERT: E 27 LEU cc_start: 0.8990 (tp) cc_final: 0.8467 (mp) REVERT: E 30 THR cc_start: 0.9656 (m) cc_final: 0.9267 (p) REVERT: H 16 LEU cc_start: 0.8464 (tp) cc_final: 0.7405 (pt) REVERT: H 22 ASN cc_start: 0.7300 (t0) cc_final: 0.6435 (p0) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.0659 time to fit residues: 3.8506 Evaluate side-chains 44 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.106223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.084578 restraints weight = 5017.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.086466 restraints weight = 2198.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.087561 restraints weight = 1369.602| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 1936 Z= 0.293 Angle : 0.623 7.638 2632 Z= 0.304 Chirality : 0.040 0.143 316 Planarity : 0.002 0.014 344 Dihedral : 6.640 38.023 312 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.40 % Allowed : 20.19 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.012 0.002 PHE B 15 ARG 0.002 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.01942 ( 61) hydrogen bonds : angle 4.56304 ( 183) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.87379 ( 8) covalent geometry : bond 0.00593 ( 1932) covalent geometry : angle 0.62209 ( 2624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1133.79 seconds wall clock time: 20 minutes 27.26 seconds (1227.26 seconds total)