Starting phenix.real_space_refine on Mon Feb 10 19:47:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykw_33897/02_2025/7ykw_33897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykw_33897/02_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_33897/02_2025/7ykw_33897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykw_33897/02_2025/7ykw_33897.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykw_33897/02_2025/7ykw_33897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykw_33897/02_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-5592/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: 1.72, per 1000 atoms: 0.90 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: 0.48 Conformation dependent library (CDL) restraints added in 211.6 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: 0.24 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: 0.46 Time building geometry restraints manager: 0.54 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: 0.380 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: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- 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 : 0.214 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: 0.0625 time to fit residues: 7.8443 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 : 0.210 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.104537 restraints weight = 1986.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.105893 restraints weight = 1144.920| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.455 Fit side-chains revert: symmetry clash REVERT: F 14 ASN cc_start: 0.7700 (m-40) cc_final: 0.7394 (t0) REVERT: H 22 ASN cc_start: 0.8321 (t0) cc_final: 0.6814 (p0) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.0596 time to fit residues: 5.7643 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 : 0.232 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** G 35 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 = 0.4237 r_free = 0.4237 target = 0.110416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.089944 restraints weight = 4914.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.092016 restraints weight = 2041.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.093286 restraints weight = 1228.469| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4535 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= 0.292 Angle : 0.585 9.348 2624 Z= 0.293 Chirality : 0.039 0.119 316 Planarity : 0.002 0.011 344 Dihedral : 5.662 18.285 312 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.92 % Allowed : 19.71 % 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: -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 0.001 0.000 HIS H 18 PHE 0.010 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: 4 poor density : 54 time to evaluate : 0.242 Fit side-chains REVERT: A 27 LEU cc_start: 0.8407 (tp) cc_final: 0.8190 (tp) REVERT: E 30 THR cc_start: 0.9604 (m) cc_final: 0.9259 (p) REVERT: H 16 LEU cc_start: 0.8221 (tp) cc_final: 0.7449 (pt) REVERT: H 22 ASN cc_start: 0.7438 (t0) cc_final: 0.6531 (p0) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.0688 time to fit residues: 5.0460 Evaluate side-chains 47 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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: 9.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN C 35 ASN F 22 ASN H 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.104810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.084736 restraints weight = 4985.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.086624 restraints weight = 2106.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.087672 restraints weight = 1273.178| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 1932 Z= 0.468 Angle : 0.622 8.651 2624 Z= 0.322 Chirality : 0.040 0.125 316 Planarity : 0.003 0.015 344 Dihedral : 7.325 19.467 312 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.85 % Allowed : 18.75 % 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: -3.98 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.012 0.002 PHE D 15 ARG 0.000 0.000 ARG D 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 56 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.222 Fit side-chains REVERT: A 15 PHE cc_start: 0.3410 (p90) cc_final: 0.3034 (p90) REVERT: H 16 LEU cc_start: 0.8314 (tp) cc_final: 0.7494 (pt) REVERT: H 22 ASN cc_start: 0.8175 (t0) cc_final: 0.6984 (p0) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.0679 time to fit residues: 4.7910 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain H residue 30 THR 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: 0.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** D 14 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 = 0.4207 r_free = 0.4207 target = 0.109157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.089421 restraints weight = 4956.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.091424 restraints weight = 2028.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.092585 restraints weight = 1212.899| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1932 Z= 0.190 Angle : 0.528 6.427 2624 Z= 0.267 Chirality : 0.039 0.131 316 Planarity : 0.002 0.015 344 Dihedral : 5.010 17.100 312 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.40 % Allowed : 23.56 % Favored : 74.04 % 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 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 18 PHE 0.008 0.001 PHE F 15 ARG 0.000 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 55 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.177 Fit side-chains REVERT: A 15 PHE cc_start: 0.3527 (p90) cc_final: 0.3222 (p90) REVERT: A 27 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7649 (pt) REVERT: B 16 LEU cc_start: 0.6729 (tp) cc_final: 0.6524 (tp) REVERT: E 30 THR cc_start: 0.9657 (m) cc_final: 0.9288 (p) REVERT: H 16 LEU cc_start: 0.8191 (tp) cc_final: 0.7256 (pt) REVERT: H 22 ASN cc_start: 0.7790 (t0) cc_final: 0.6689 (p0) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.0689 time to fit residues: 4.8985 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain D residue 6 THR 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: 3.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 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 = 0.4183 r_free = 0.4183 target = 0.107176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.086345 restraints weight = 5005.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.088327 restraints weight = 2102.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.089309 restraints weight = 1277.567| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1932 Z= 0.312 Angle : 0.581 9.296 2624 Z= 0.286 Chirality : 0.040 0.164 316 Planarity : 0.002 0.014 344 Dihedral : 5.915 23.891 312 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.85 % Allowed : 20.67 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.24 (0.38), 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 0.002 0.000 HIS H 18 PHE 0.009 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 55 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.228 Fit side-chains REVERT: D 14 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.6854 (t0) REVERT: E 30 THR cc_start: 0.9658 (m) cc_final: 0.9281 (p) REVERT: H 22 ASN cc_start: 0.8092 (t0) cc_final: 0.6935 (p0) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.0631 time to fit residues: 4.5805 Evaluate side-chains 50 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 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 = 0.4218 r_free = 0.4218 target = 0.122638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.089800 restraints weight = 5233.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.092036 restraints weight = 2254.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.093365 restraints weight = 1403.311| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 1932 Z= 0.401 Angle : 0.604 7.001 2624 Z= 0.304 Chirality : 0.041 0.176 316 Planarity : 0.002 0.014 344 Dihedral : 6.512 30.380 312 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.88 % Allowed : 23.08 % Favored : 74.04 % 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: -4.33 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (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 D 15 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 52 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.247 Fit side-chains REVERT: A 27 LEU cc_start: 0.8625 (tp) cc_final: 0.7396 (pt) REVERT: C 27 LEU cc_start: 0.8886 (tp) cc_final: 0.8670 (tp) REVERT: E 30 THR cc_start: 0.9657 (m) cc_final: 0.9255 (p) REVERT: H 16 LEU cc_start: 0.8211 (tp) cc_final: 0.7204 (pt) REVERT: H 22 ASN cc_start: 0.8245 (t0) cc_final: 0.7078 (p0) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.0604 time to fit residues: 4.1979 Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 17 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.126476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.093958 restraints weight = 5295.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.096359 restraints weight = 2259.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.097798 restraints weight = 1368.386| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.6292 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= 0.179 Angle : 0.561 7.797 2624 Z= 0.270 Chirality : 0.041 0.163 316 Planarity : 0.002 0.011 344 Dihedral : 5.162 26.041 312 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.92 % Allowed : 24.04 % Favored : 74.04 % 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 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 18 PHE 0.006 0.001 PHE B 15 ARG 0.000 0.000 ARG F 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 51 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.213 Fit side-chains REVERT: A 27 LEU cc_start: 0.8723 (tp) cc_final: 0.7431 (pt) REVERT: E 30 THR cc_start: 0.9640 (m) cc_final: 0.9283 (p) REVERT: H 16 LEU cc_start: 0.7751 (tp) cc_final: 0.6898 (pt) REVERT: H 22 ASN cc_start: 0.8042 (t0) cc_final: 0.6881 (p0) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0661 time to fit residues: 4.4487 Evaluate side-chains 48 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 17 VAL 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: 3.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.107038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.084632 restraints weight = 5093.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.086779 restraints weight = 2223.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.087971 restraints weight = 1354.683| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 1932 Z= 0.415 Angle : 0.637 7.554 2624 Z= 0.315 Chirality : 0.042 0.183 316 Planarity : 0.002 0.014 344 Dihedral : 6.741 34.373 312 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.88 % Allowed : 21.15 % 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: -4.40 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.011 0.002 PHE B 15 ARG 0.001 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 50 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.233 Fit side-chains REVERT: A 27 LEU cc_start: 0.8752 (tp) cc_final: 0.7320 (pt) REVERT: E 30 THR cc_start: 0.9692 (m) cc_final: 0.9281 (p) REVERT: H 16 LEU cc_start: 0.8107 (tp) cc_final: 0.7116 (pt) REVERT: H 22 ASN cc_start: 0.8294 (t0) cc_final: 0.7095 (p0) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.0621 time to fit residues: 4.0541 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 : 0.224 ------------------------------------------------------------------------------- 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: 10.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.128819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.092345 restraints weight = 5252.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.094660 restraints weight = 2320.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.096043 restraints weight = 1447.603| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1932 Z= 0.226 Angle : 0.568 8.131 2624 Z= 0.274 Chirality : 0.041 0.174 316 Planarity : 0.002 0.010 344 Dihedral : 5.553 30.295 312 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.92 % Allowed : 23.56 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.37 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.010 0.001 PHE F 15 ARG 0.000 0.000 ARG D 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 52 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.220 Fit side-chains REVERT: A 27 LEU cc_start: 0.8721 (tp) cc_final: 0.7459 (pt) REVERT: E 30 THR cc_start: 0.9660 (m) cc_final: 0.9263 (p) REVERT: H 16 LEU cc_start: 0.7732 (tp) cc_final: 0.6902 (pt) REVERT: H 22 ASN cc_start: 0.7367 (t0) cc_final: 0.6439 (p0) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.0754 time to fit residues: 4.9767 Evaluate side-chains 50 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU 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: 2.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.107186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.085166 restraints weight = 4940.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.087184 restraints weight = 2222.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.088327 restraints weight = 1376.434| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1932 Z= 0.376 Angle : 0.631 7.701 2624 Z= 0.311 Chirality : 0.041 0.180 316 Planarity : 0.002 0.012 344 Dihedral : 6.492 35.599 312 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.40 % Allowed : 22.60 % Favored : 75.00 % 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: -4.42 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.010 0.001 PHE B 15 ARG 0.001 0.000 ARG H 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.00 seconds wall clock time: 19 minutes 19.94 seconds (1159.94 seconds total)