Starting phenix.real_space_refine on Wed Mar 5 14:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykw_33897/03_2025/7ykw_33897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykw_33897/03_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_33897/03_2025/7ykw_33897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_2025/7ykw_33897.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_2025/7ykw_33897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykw_33897/03_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-5624/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: 1.93, per 1000 atoms: 1.01 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: 0.51 Conformation dependent library (CDL) restraints added in 470.4 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: 0.28 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: 0.47 Time building geometry restraints manager: 0.60 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: 0.370 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.870 Find NCS groups from input model: 0.060 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- 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 1932 Z= 0.645 Angle : 1.663 8.448 2624 Z= 1.048 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 *********************** 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 : 0.229 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: 0.0613 time to fit residues: 7.7315 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 : 0.168 ------------------------------------------------------------------------------- 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 1932 Z= 0.216 Angle : 0.625 9.272 2624 Z= 0.305 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 *********************** 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 : 0.216 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: 0.0735 time to fit residues: 6.8084 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 : 0.240 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 22 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 = 0.4253 r_free = 0.4253 target = 0.111218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090717 restraints weight = 4885.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.092804 restraints weight = 2057.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.094090 restraints weight = 1244.133| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1932 Z= 0.278 Angle : 0.579 9.195 2624 Z= 0.290 Chirality : 0.040 0.120 316 Planarity : 0.002 0.011 344 Dihedral : 5.587 18.186 312 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.96 % Allowed : 20.19 % 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: -3.86 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.011 0.001 PHE B 15 ARG 0.001 0.000 ARG D 11 *********************** 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 58 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.235 Fit side-chains REVERT: E 30 THR cc_start: 0.9614 (m) cc_final: 0.9243 (p) REVERT: H 16 LEU cc_start: 0.8102 (tp) cc_final: 0.7401 (pt) REVERT: H 22 ASN cc_start: 0.7415 (t0) cc_final: 0.6541 (p0) outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.0660 time to fit residues: 4.9377 Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN F 22 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 = 0.4234 r_free = 0.4234 target = 0.110109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.090352 restraints weight = 4818.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.092452 restraints weight = 2048.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.093482 restraints weight = 1217.086| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1932 Z= 0.296 Angle : 0.534 6.080 2624 Z= 0.278 Chirality : 0.039 0.114 316 Planarity : 0.002 0.012 344 Dihedral : 5.721 18.432 312 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.88 % Allowed : 19.71 % 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: -3.95 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.009 0.002 PHE G 23 ARG 0.000 0.000 ARG C 11 *********************** 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: 6 poor density : 49 time to evaluate : 0.230 Fit side-chains REVERT: E 30 THR cc_start: 0.9638 (m) cc_final: 0.9284 (p) REVERT: H 16 LEU cc_start: 0.8231 (tp) cc_final: 0.7379 (pt) REVERT: H 22 ASN cc_start: 0.7884 (t0) cc_final: 0.6712 (p0) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.0631 time to fit residues: 4.4828 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 : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 6 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 0.0670 chunk 12 optimal weight: 8.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.117350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.094447 restraints weight = 4953.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.096846 restraints weight = 2020.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.098188 restraints weight = 1188.268| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1932 Z= 0.210 Angle : 0.542 9.048 2624 Z= 0.267 Chirality : 0.039 0.117 316 Planarity : 0.002 0.016 344 Dihedral : 4.949 16.720 312 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.88 % Allowed : 20.19 % 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: -4.09 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 18 PHE 0.005 0.001 PHE G 23 ARG 0.001 0.000 ARG F 11 *********************** 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 57 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.218 Fit side-chains REVERT: A 23 PHE cc_start: 0.9202 (m-80) cc_final: 0.6799 (p90) REVERT: B 16 LEU cc_start: 0.7522 (tp) cc_final: 0.7263 (tp) REVERT: E 27 LEU cc_start: 0.8973 (tp) cc_final: 0.8771 (tt) REVERT: E 30 THR cc_start: 0.9628 (m) cc_final: 0.9265 (p) REVERT: H 16 LEU cc_start: 0.8215 (tp) cc_final: 0.7265 (pt) REVERT: H 22 ASN cc_start: 0.7855 (t0) cc_final: 0.6728 (p0) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.0615 time to fit residues: 4.4422 Evaluate side-chains 51 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 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 = 0.4259 r_free = 0.4259 target = 0.111836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.091811 restraints weight = 4901.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.093885 restraints weight = 2039.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.095081 restraints weight = 1225.639| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1932 Z= 0.224 Angle : 0.535 8.619 2624 Z= 0.264 Chirality : 0.039 0.120 316 Planarity : 0.002 0.011 344 Dihedral : 5.056 19.734 312 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.40 % Allowed : 19.71 % Favored : 77.88 % 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: -4.15 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (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 G 23 ARG 0.001 0.000 ARG H 11 *********************** 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 51 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.223 Fit side-chains REVERT: A 23 PHE cc_start: 0.9186 (m-80) cc_final: 0.6877 (p90) REVERT: E 30 THR cc_start: 0.9645 (m) cc_final: 0.9286 (p) REVERT: H 16 LEU cc_start: 0.8198 (tp) cc_final: 0.7261 (pt) REVERT: H 22 ASN cc_start: 0.7844 (t0) cc_final: 0.6696 (p0) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.0644 time to fit residues: 4.2776 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 : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F 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: 30.0000 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.4229 r_free = 0.4229 target = 0.124473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.090544 restraints weight = 5228.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.092653 restraints weight = 2243.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.093969 restraints weight = 1388.384| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 1932 Z= 0.491 Angle : 0.615 6.708 2624 Z= 0.320 Chirality : 0.039 0.118 316 Planarity : 0.003 0.016 344 Dihedral : 7.206 32.134 312 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.88 % Allowed : 19.71 % 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: -4.23 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.015 0.002 PHE G 23 ARG 0.001 0.000 ARG H 11 *********************** 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 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.221 Fit side-chains REVERT: H 16 LEU cc_start: 0.8500 (tp) cc_final: 0.7380 (pt) REVERT: H 22 ASN cc_start: 0.8306 (t0) cc_final: 0.7133 (p0) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0654 time to fit residues: 4.0486 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F 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: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.0000 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.110302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.089603 restraints weight = 5049.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.091564 restraints weight = 2135.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.092750 restraints weight = 1278.294| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1932 Z= 0.233 Angle : 0.531 7.649 2624 Z= 0.264 Chirality : 0.038 0.117 316 Planarity : 0.002 0.009 344 Dihedral : 5.428 28.511 312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.44 % Allowed : 20.67 % Favored : 77.88 % 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 0.002 0.000 HIS H 18 PHE 0.007 0.001 PHE B 15 ARG 0.000 0.000 ARG H 11 *********************** 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 49 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.185 Fit side-chains REVERT: A 23 PHE cc_start: 0.9237 (m-80) cc_final: 0.7114 (p90) REVERT: E 30 THR cc_start: 0.9652 (m) cc_final: 0.9309 (p) REVERT: H 16 LEU cc_start: 0.8157 (tp) cc_final: 0.7247 (pt) REVERT: H 22 ASN cc_start: 0.8056 (t0) cc_final: 0.6832 (p0) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.0783 time to fit residues: 5.1004 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F 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: 10.0000 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.110711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.089414 restraints weight = 5147.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.091489 restraints weight = 2173.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.092523 restraints weight = 1295.500| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1932 Z= 0.250 Angle : 0.538 7.795 2624 Z= 0.266 Chirality : 0.039 0.121 316 Planarity : 0.002 0.010 344 Dihedral : 5.497 29.211 312 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -4.32 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.010 0.001 PHE D 15 ARG 0.000 0.000 ARG H 11 *********************** 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 46 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.263 Fit side-chains REVERT: E 30 THR cc_start: 0.9656 (m) cc_final: 0.9266 (p) REVERT: H 16 LEU cc_start: 0.8159 (tp) cc_final: 0.7262 (pt) REVERT: H 22 ASN cc_start: 0.8057 (t0) cc_final: 0.6845 (p0) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.0610 time to fit residues: 3.8341 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 : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 6 THR 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: 9.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.126413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.089504 restraints weight = 5350.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.091621 restraints weight = 2330.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.092916 restraints weight = 1451.782| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 1932 Z= 0.486 Angle : 0.624 7.466 2624 Z= 0.322 Chirality : 0.041 0.131 316 Planarity : 0.002 0.012 344 Dihedral : 7.115 38.101 312 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.40 % Allowed : 19.71 % Favored : 77.88 % 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: -4.46 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.27), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.014 0.002 PHE G 23 ARG 0.001 0.000 ARG H 11 ********************** 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 46 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.236 Fit side-chains REVERT: H 16 LEU cc_start: 0.8429 (tp) cc_final: 0.7305 (pt) REVERT: H 22 ASN cc_start: 0.8296 (t0) cc_final: 0.7092 (p0) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.0877 time to fit residues: 5.0876 Evaluate side-chains 41 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 6 THR 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: 20.0000 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.110558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.088844 restraints weight = 4926.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.090807 restraints weight = 2239.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.091922 restraints weight = 1388.053| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1932 Z= 0.240 Angle : 0.572 8.135 2624 Z= 0.281 Chirality : 0.041 0.134 316 Planarity : 0.002 0.010 344 Dihedral : 5.930 34.093 312 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.92 % Allowed : 21.15 % 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: -4.49 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.008 0.001 PHE B 15 ARG 0.000 0.000 ARG H 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1061.36 seconds wall clock time: 19 minutes 29.22 seconds (1169.22 seconds total)