Starting phenix.real_space_refine on Fri Dec 27 04:18:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykw_33897/12_2024/7ykw_33897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykw_33897/12_2024/7ykw_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_33897/12_2024/7ykw_33897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykw_33897/12_2024/7ykw_33897.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykw_33897/12_2024/7ykw_33897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykw_33897/12_2024/7ykw_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-5532/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: 1.89, per 1000 atoms: 0.99 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: 0.50 Conformation dependent library (CDL) restraints added in 220.4 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: 0.24 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: 0.43 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 636 1.33 - 1.45: 405 1.45 - 1.57: 883 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 1932 Sorted by residual: bond pdb=" C THR D 36 " pdb=" N TYC D 37 " ideal model delta sigma weight residual 1.329 1.261 0.068 1.40e-02 5.10e+03 2.33e+01 bond pdb=" C THR B 36 " pdb=" N TYC B 37 " ideal model delta sigma weight residual 1.329 1.262 0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" C THR F 36 " pdb=" N TYC F 37 " ideal model delta sigma weight residual 1.329 1.263 0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" C THR H 36 " pdb=" N TYC H 37 " ideal model delta sigma weight residual 1.329 1.263 0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C THR G 36 " pdb=" N TYC G 37 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.40e-02 5.10e+03 9.62e+00 ... (remaining 1927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 2143 1.69 - 3.38: 299 3.38 - 5.07: 136 5.07 - 6.76: 25 6.76 - 8.45: 21 Bond angle restraints: 2624 Sorted by residual: angle pdb=" N ALA D 5 " pdb=" CA ALA D 5 " pdb=" C ALA D 5 " ideal model delta sigma weight residual 111.36 104.26 7.10 1.09e+00 8.42e-01 4.24e+01 angle pdb=" N ALA F 5 " pdb=" CA ALA F 5 " pdb=" C ALA F 5 " ideal model delta sigma weight residual 111.28 105.14 6.14 1.09e+00 8.42e-01 3.17e+01 angle pdb=" N PHE F 23 " pdb=" CA PHE F 23 " pdb=" C PHE F 23 " ideal model delta sigma weight residual 108.49 100.04 8.45 1.65e+00 3.67e-01 2.62e+01 angle pdb=" N PHE B 23 " pdb=" CA PHE B 23 " pdb=" C PHE B 23 " ideal model delta sigma weight residual 108.49 100.06 8.43 1.65e+00 3.67e-01 2.61e+01 angle pdb=" N PHE D 23 " pdb=" CA PHE D 23 " pdb=" C PHE D 23 " ideal model delta sigma weight residual 108.49 100.07 8.42 1.65e+00 3.67e-01 2.60e+01 ... (remaining 2619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 1040 13.40 - 26.80: 68 26.80 - 40.20: 33 40.20 - 53.60: 12 53.60 - 67.00: 3 Dihedral angle restraints: 1156 sinusoidal: 428 harmonic: 728 Sorted by residual: dihedral pdb=" CB CYS D 2 " pdb=" SG CYS D 2 " pdb=" SG CYS D 7 " pdb=" CB CYS D 7 " ideal model delta sinusoidal sigma weight residual -86.00 -153.00 67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -142.11 56.11 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS H 2 " pdb=" SG CYS H 2 " pdb=" SG CYS H 7 " pdb=" CB CYS H 7 " ideal model delta sinusoidal sigma weight residual -86.00 -141.48 55.48 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 1153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 150 0.047 - 0.095: 83 0.095 - 0.142: 43 0.142 - 0.189: 24 0.189 - 0.236: 16 Chirality restraints: 316 Sorted by residual: chirality pdb=" CA PHE F 23 " pdb=" N PHE F 23 " pdb=" C PHE F 23 " pdb=" CB PHE F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE B 23 " pdb=" N PHE B 23 " pdb=" C PHE B 23 " pdb=" CB PHE B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE D 23 " pdb=" N PHE D 23 " pdb=" C PHE D 23 " pdb=" CB PHE D 23 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 313 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 36 " -0.017 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C THR A 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC A 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 36 " -0.017 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C THR C 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC C 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " -0.017 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C THR E 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1213 3.01 - 3.48: 1824 3.48 - 3.96: 3224 3.96 - 4.43: 3548 4.43 - 4.90: 6479 Nonbonded interactions: 16288 Sorted by model distance: nonbonded pdb=" N ASN F 3 " pdb=" N THR F 4 " model vdw 2.538 2.560 nonbonded pdb=" N ASN B 3 " pdb=" N THR B 4 " model vdw 2.547 2.560 nonbonded pdb=" C THR B 4 " pdb=" OG1 THR B 4 " model vdw 2.561 2.616 nonbonded pdb=" N ASN D 3 " pdb=" N THR D 4 " model vdw 2.567 2.560 nonbonded pdb=" N ASN B 3 " pdb=" O CYS D 2 " model vdw 2.568 3.120 ... (remaining 16283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.080 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- 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 : 0.223 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: 0.0741 time to fit residues: 9.4768 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 : 0.307 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.244 Fit side-chains revert: symmetry clash REVERT: G 22 ASN cc_start: 0.7488 (t0) cc_final: 0.7275 (t0) REVERT: H 22 ASN cc_start: 0.6816 (t0) cc_final: 0.5410 (p0) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.0628 time to fit residues: 5.8262 Evaluate side-chains 54 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1932 Z= 0.229 Angle : 0.574 9.233 2624 Z= 0.282 Chirality : 0.040 0.115 316 Planarity : 0.002 0.011 344 Dihedral : 5.120 17.942 312 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 19.71 % 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: -3.82 (0.40), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 18 PHE 0.007 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 61 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.187 Fit side-chains REVERT: E 30 THR cc_start: 0.9259 (m) cc_final: 0.8942 (p) REVERT: G 28 SER cc_start: 0.8660 (t) cc_final: 0.8382 (p) REVERT: H 16 LEU cc_start: 0.7463 (tp) cc_final: 0.6720 (pt) outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 0.0671 time to fit residues: 5.1739 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 : 0.231 ------------------------------------------------------------------------------- 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 9 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN C 35 ASN F 22 ASN H 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1932 Z= 0.382 Angle : 0.591 8.675 2624 Z= 0.305 Chirality : 0.040 0.118 316 Planarity : 0.002 0.013 344 Dihedral : 6.531 18.574 312 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.85 % Allowed : 16.83 % 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: -3.94 (0.40), 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 0.004 0.001 HIS H 18 PHE 0.012 0.002 PHE B 15 ARG 0.001 0.000 ARG H 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 57 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.296 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.0721 time to fit residues: 5.3644 Evaluate side-chains 49 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 H residue 27 LEU 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 17 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1932 Z= 0.232 Angle : 0.541 8.315 2624 Z= 0.271 Chirality : 0.039 0.121 316 Planarity : 0.002 0.015 344 Dihedral : 5.153 16.635 312 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.44 % Allowed : 21.63 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.30), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.009 0.001 PHE F 15 ARG 0.000 0.000 ARG D 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 50 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.235 Fit side-chains REVERT: E 27 LEU cc_start: 0.8688 (tp) cc_final: 0.8380 (tp) REVERT: E 30 THR cc_start: 0.9335 (m) cc_final: 0.9025 (p) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0658 time to fit residues: 4.3223 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain F residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5856 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= 0.486 Angle : 0.631 8.121 2624 Z= 0.325 Chirality : 0.040 0.120 316 Planarity : 0.003 0.016 344 Dihedral : 7.270 28.456 312 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.40 % Allowed : 20.19 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 18 PHE 0.014 0.002 PHE G 23 ARG 0.001 0.000 ARG D 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 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.217 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.0611 time to fit residues: 3.5733 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 : 0.244 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 3 ASN H 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1932 Z= 0.202 Angle : 0.531 7.190 2624 Z= 0.264 Chirality : 0.039 0.127 316 Planarity : 0.002 0.011 344 Dihedral : 5.311 20.812 312 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.32 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: -4.30 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.008 0.001 PHE G 23 ARG 0.000 0.000 ARG D 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 47 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.219 Fit side-chains REVERT: A 23 PHE cc_start: 0.8135 (m-80) cc_final: 0.6524 (p90) REVERT: E 30 THR cc_start: 0.9370 (m) cc_final: 0.9046 (p) REVERT: H 16 LEU cc_start: 0.7043 (tp) cc_final: 0.6202 (pt) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.0561 time to fit residues: 3.5564 Evaluate side-chains 42 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 0.031 1932 Z= 0.210 Angle : 0.524 7.572 2624 Z= 0.262 Chirality : 0.039 0.126 316 Planarity : 0.002 0.011 344 Dihedral : 5.231 22.019 312 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.40 % Allowed : 20.19 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.009 0.001 PHE D 15 ARG 0.001 0.000 ARG D 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 47 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.224 Fit side-chains REVERT: E 30 THR cc_start: 0.9357 (m) cc_final: 0.9032 (p) outliers start: 5 outliers final: 5 residues processed: 45 average time/residue: 0.0612 time to fit residues: 3.7388 Evaluate side-chains 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 F residue 26 ILE 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 12 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6508 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= 0.185 Angle : 0.534 7.866 2624 Z= 0.260 Chirality : 0.040 0.126 316 Planarity : 0.002 0.010 344 Dihedral : 4.901 22.678 312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.92 % Allowed : 20.67 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.008 0.001 PHE D 15 ARG 0.000 0.000 ARG F 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 45 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.242 Fit side-chains REVERT: D 14 ASN cc_start: 0.6989 (m-40) cc_final: 0.6744 (m-40) REVERT: E 30 THR cc_start: 0.9335 (m) cc_final: 0.9025 (p) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0579 time to fit residues: 3.5032 Evaluate side-chains 42 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1932 Z= 0.191 Angle : 0.563 8.158 2624 Z= 0.266 Chirality : 0.040 0.139 316 Planarity : 0.002 0.010 344 Dihedral : 4.869 23.482 312 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.40 % Allowed : 20.67 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.31 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 18 PHE 0.008 0.001 PHE F 15 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 44 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.236 Fit side-chains REVERT: E 30 THR cc_start: 0.9309 (m) cc_final: 0.9016 (p) outliers start: 5 outliers final: 5 residues processed: 42 average time/residue: 0.0682 time to fit residues: 3.9681 Evaluate side-chains 44 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.132808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.094423 restraints weight = 5243.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.096539 restraints weight = 2221.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.097662 restraints weight = 1384.629| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 1932 Z= 0.403 Angle : 0.623 7.557 2624 Z= 0.306 Chirality : 0.040 0.133 316 Planarity : 0.002 0.014 344 Dihedral : 6.466 33.846 312 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.40 % Allowed : 21.15 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.36), 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 0.004 0.001 HIS H 18 PHE 0.012 0.002 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: 850.01 seconds wall clock time: 16 minutes 23.43 seconds (983.43 seconds total)