Starting phenix.real_space_refine on Tue Aug 4 12:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oi9_70514/08_2026/9oi9_70514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oi9_70514/08_2026/9oi9_70514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oi9_70514/08_2026/9oi9_70514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oi9_70514/08_2026/9oi9_70514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oi9_70514/08_2026/9oi9_70514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oi9_70514/08_2026/9oi9_70514.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 30 5.16 5 C 2085 2.51 5 N 510 2.21 5 O 525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3150 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 210 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 0.58, per 1000 atoms: 0.18 Number of scatterers: 3150 At special positions: 0 Unit cell: (75.624, 73.98, 37.812, 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 30 16.00 O 525 8.00 N 510 7.00 C 2085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 22 " distance=2.04 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 22 " distance=2.04 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 22 " distance=2.04 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 22 " distance=2.04 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 22 " distance=2.04 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 22 " distance=2.04 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 22 " distance=2.04 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 22 " distance=2.04 Simple disulfide: pdb=" SG CYS K 5 " - pdb=" SG CYS K 22 " distance=2.04 Simple disulfide: pdb=" SG CYS L 5 " - pdb=" SG CYS L 22 " distance=2.04 Simple disulfide: pdb=" SG CYS M 5 " - pdb=" SG CYS M 22 " distance=2.04 Simple disulfide: pdb=" SG CYS N 5 " - pdb=" SG CYS N 22 " distance=2.04 Simple disulfide: pdb=" SG CYS O 5 " - pdb=" SG CYS O 22 " distance=2.04 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: 0.28 Conformation dependent library (CDL) restraints added in 128.4 milliseconds 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.965A pdb=" N PHE D 11 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS G 14 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN D 13 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE A 11 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS D 14 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN A 13 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 21 through 26 removed outlier: 8.138A pdb=" N ILE D 21 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASN G 24 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE D 23 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE G 26 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU D 25 " --> pdb=" O PHE G 26 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 21 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN D 24 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 23 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N PHE D 26 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 25 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE J 23 " --> pdb=" O CYS A 22 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A 24 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE M 23 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN J 24 " --> pdb=" O PHE M 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.918A pdb=" N PHE E 11 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LYS H 14 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN E 13 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 11 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LYS E 14 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 13 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 21 through 26 removed outlier: 8.161A pdb=" N ILE E 21 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASN H 24 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE E 23 " --> pdb=" O ASN H 24 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N PHE H 26 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU E 25 " --> pdb=" O PHE H 26 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE B 21 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN E 24 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE B 23 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE E 26 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 25 " --> pdb=" O PHE E 26 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE K 23 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 24 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE N 23 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN K 24 " --> pdb=" O PHE N 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.909A pdb=" N PHE C 11 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LYS F 14 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN C 13 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE I 11 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS O 14 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN I 13 " --> pdb=" O LYS O 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 21 through 26 removed outlier: 8.142A pdb=" N ILE C 21 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ASN F 24 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE C 23 " --> pdb=" O ASN F 24 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE F 26 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU C 25 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE O 23 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN C 24 " --> pdb=" O PHE O 23 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE I 21 " --> pdb=" O CYS O 22 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASN O 24 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE I 23 " --> pdb=" O ASN O 24 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N PHE O 26 " --> pdb=" O PHE I 23 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU I 25 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE L 23 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN I 24 " --> pdb=" O PHE L 23 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 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: 0.39 Time building geometry restraints manager: 0.37 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: 844 1.33 - 1.45: 685 1.45 - 1.58: 1666 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 3225 Sorted by residual: bond pdb=" N SER F 3 " pdb=" CA SER F 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N SER E 3 " pdb=" CA SER E 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N SER N 3 " pdb=" CA SER N 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N SER K 3 " pdb=" CA SER K 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N SER C 3 " pdb=" CA SER C 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 3220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 3547 1.68 - 3.35: 683 3.35 - 5.02: 60 5.02 - 6.70: 0 6.70 - 8.37: 45 Bond angle restraints: 4335 Sorted by residual: angle pdb=" CA CYS I 5 " pdb=" CB CYS I 5 " pdb=" SG CYS I 5 " ideal model delta sigma weight residual 114.40 122.28 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CA CYS E 5 " pdb=" CB CYS E 5 " pdb=" SG CYS E 5 " ideal model delta sigma weight residual 114.40 122.27 -7.87 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CA CYS L 5 " pdb=" CB CYS L 5 " pdb=" SG CYS L 5 " ideal model delta sigma weight residual 114.40 122.27 -7.87 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CA CYS K 5 " pdb=" CB CYS K 5 " pdb=" SG CYS K 5 " ideal model delta sigma weight residual 114.40 122.27 -7.87 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CA CYS O 5 " pdb=" CB CYS O 5 " pdb=" SG CYS O 5 " ideal model delta sigma weight residual 114.40 122.27 -7.87 2.30e+00 1.89e-01 1.17e+01 ... (remaining 4330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.19: 1380 11.19 - 22.37: 300 22.37 - 33.55: 105 33.55 - 44.73: 45 44.73 - 55.91: 60 Dihedral angle restraints: 1890 sinusoidal: 780 harmonic: 1110 Sorted by residual: dihedral pdb=" CA ASN I 4 " pdb=" C ASN I 4 " pdb=" N CYS I 5 " pdb=" CA CYS I 5 " ideal model delta harmonic sigma weight residual 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN M 4 " pdb=" C ASN M 4 " pdb=" N CYS M 5 " pdb=" CA CYS M 5 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN G 4 " pdb=" C ASN G 4 " pdb=" N CYS G 5 " pdb=" CA CYS G 5 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 1887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 96 0.032 - 0.064: 180 0.064 - 0.096: 84 0.096 - 0.128: 60 0.128 - 0.160: 60 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA PHE L 23 " pdb=" N PHE L 23 " pdb=" C PHE L 23 " pdb=" CB PHE L 23 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 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 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CG LEU E 25 " pdb=" CB LEU E 25 " pdb=" CD1 LEU E 25 " pdb=" CD2 LEU E 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 477 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS H 22 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.87e+00 pdb=" C CYS H 22 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS H 22 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE H 23 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 22 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C CYS F 22 " 0.048 2.00e-02 2.50e+03 pdb=" O CYS F 22 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE F 23 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS L 22 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C CYS L 22 " 0.048 2.00e-02 2.50e+03 pdb=" O CYS L 22 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE L 23 " -0.017 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1076 2.89 - 3.39: 2900 3.39 - 3.89: 5327 3.89 - 4.40: 6538 4.40 - 4.90: 11344 Nonbonded interactions: 27185 Sorted by model distance: nonbonded pdb=" O THR K 19 " pdb=" OG1 THR N 19 " model vdw 2.383 3.040 nonbonded pdb=" O THR I 19 " pdb=" OG1 THR L 19 " model vdw 2.389 3.040 nonbonded pdb=" O THR J 19 " pdb=" OG1 THR M 19 " model vdw 2.428 3.040 nonbonded pdb=" OG1 THR A 19 " pdb=" O THR D 19 " model vdw 2.451 3.040 nonbonded pdb=" OG1 THR B 19 " pdb=" O THR E 19 " model vdw 2.456 3.040 ... (remaining 27180 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic 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: 1.690 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: 0.010 Set scattering table: 0.010 Process input model: 5.030 Find NCS groups from input model: 0.030 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:5.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.009 0.041 3240 Z= 0.434 Angle : 1.508 8.374 4365 Z= 0.840 Chirality : 0.081 0.160 480 Planarity : 0.010 0.031 555 Dihedral : 17.812 55.914 1095 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.74 % Favored : 78.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.25 (0.27), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.21), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 9 PHE 0.024 0.006 PHE B 23 HIS 0.007 0.004 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.43 ( 3225) covalent geometry : angle 1.49363 / 0.84 ( 4335) SS BOND : bond 0.00772 / 0.47 ( 15) SS BOND : angle 2.88362 / 1.99 ( 30) hydrogen bonds : bond 0.20196 / 13.21 ( 42) hydrogen bonds : angle 7.55666 / 5.24 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.117 Fit side-chains REVERT: O 25 LEU cc_start: 0.8763 (mm) cc_final: 0.8446 (mm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.5263 time to fit residues: 24.9867 Evaluate side-chains 39 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN B 4 ASN C 4 ASN D 4 ASN E 4 ASN I 4 ASN J 4 ASN K 4 ASN L 4 ASN M 4 ASN N 4 ASN O 4 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.176355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.166913 restraints weight = 3649.629| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 1.67 r_work: 0.4204 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3240 Z= 0.149 Angle : 0.738 6.243 4365 Z= 0.360 Chirality : 0.048 0.108 480 Planarity : 0.003 0.014 555 Dihedral : 9.876 40.004 390 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 2.61 % Allowed : 11.88 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.54 (0.21), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.98 (0.16), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 9 PHE 0.011 0.002 PHE A 23 HIS 0.002 0.001 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3225) covalent geometry : angle 0.73885 / 0.36 ( 4335) SS BOND : bond 0.00275 / 0.17 ( 15) SS BOND : angle 0.65362 / 0.44 ( 30) hydrogen bonds : bond 0.02537 / 1.59 ( 42) hydrogen bonds : angle 4.69133 / 3.38 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.089 Fit side-chains REVERT: A 25 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8379 (mm) outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 0.6668 time to fit residues: 39.6062 Evaluate side-chains 57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain E residue 3 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.175015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.165593 restraints weight = 3739.894| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.66 r_work: 0.4193 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3240 Z= 0.120 Angle : 0.669 5.959 4365 Z= 0.320 Chirality : 0.045 0.100 480 Planarity : 0.003 0.024 555 Dihedral : 8.792 36.444 390 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 1.74 % Allowed : 21.45 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.39 (0.22), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 9 PHE 0.008 0.001 PHE A 23 HIS 0.002 0.000 HIS H 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3225) covalent geometry : angle 0.67012 / 0.32 ( 4335) SS BOND : bond 0.00086 / 0.06 ( 15) SS BOND : angle 0.48815 / 0.32 ( 30) hydrogen bonds : bond 0.01931 / 1.19 ( 42) hydrogen bonds : angle 4.63678 / 3.29 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.127 Fit side-chains REVERT: L 6 PHE cc_start: 0.8251 (m-10) cc_final: 0.8029 (m-10) REVERT: N 6 PHE cc_start: 0.8303 (m-10) cc_final: 0.8087 (m-10) REVERT: N 9 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7838 (ttt90) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.7075 time to fit residues: 46.3215 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain E residue 3 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 6 optimal weight: 0.0070 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.181422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.171911 restraints weight = 3703.037| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.64 r_work: 0.4249 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3240 Z= 0.097 Angle : 0.610 6.391 4365 Z= 0.291 Chirality : 0.044 0.104 480 Planarity : 0.003 0.022 555 Dihedral : 7.722 32.105 390 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 1.16 % Allowed : 28.12 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.32 (0.22), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.81 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 9 PHE 0.009 0.001 PHE B 23 HIS 0.002 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 3225) covalent geometry : angle 0.61132 / 0.29 ( 4335) SS BOND : bond 0.00082 / 0.05 ( 15) SS BOND : angle 0.46856 / 0.30 ( 30) hydrogen bonds : bond 0.01684 / 1.06 ( 42) hydrogen bonds : angle 4.82577 / 3.52 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.131 Fit side-chains REVERT: L 6 PHE cc_start: 0.8126 (m-10) cc_final: 0.7862 (m-10) REVERT: N 6 PHE cc_start: 0.8102 (m-10) cc_final: 0.7839 (m-10) REVERT: N 9 ARG cc_start: 0.8007 (ttt90) cc_final: 0.7779 (ttt90) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.6666 time to fit residues: 45.0819 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.0020 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.177147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.167709 restraints weight = 3769.336| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 1.65 r_work: 0.4215 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4123 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3240 Z= 0.104 Angle : 0.596 6.112 4365 Z= 0.290 Chirality : 0.043 0.101 480 Planarity : 0.003 0.017 555 Dihedral : 7.308 29.986 390 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 1.45 % Allowed : 28.99 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.35 (0.23), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.84 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 9 PHE 0.009 0.001 PHE B 23 HIS 0.002 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 3225) covalent geometry : angle 0.59706 / 0.29 ( 4335) SS BOND : bond 0.00091 / 0.06 ( 15) SS BOND : angle 0.46103 / 0.29 ( 30) hydrogen bonds : bond 0.01702 / 1.06 ( 42) hydrogen bonds : angle 4.86041 / 3.46 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.124 Fit side-chains REVERT: L 6 PHE cc_start: 0.8176 (m-10) cc_final: 0.7952 (m-10) REVERT: N 6 PHE cc_start: 0.8216 (m-10) cc_final: 0.7966 (OUTLIER) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.6728 time to fit residues: 45.5026 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain I residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 4 ASN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.173067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.163852 restraints weight = 3816.629| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 1.64 r_work: 0.4183 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3240 Z= 0.116 Angle : 0.607 8.627 4365 Z= 0.298 Chirality : 0.043 0.100 480 Planarity : 0.003 0.016 555 Dihedral : 7.245 29.165 390 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.03 % Allowed : 31.88 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.35 (0.23), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.84 (0.17), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 9 PHE 0.009 0.001 PHE B 23 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3225) covalent geometry : angle 0.60760 / 0.30 ( 4335) SS BOND : bond 0.00107 / 0.07 ( 15) SS BOND : angle 0.51278 / 0.32 ( 30) hydrogen bonds : bond 0.01789 / 1.17 ( 42) hydrogen bonds : angle 4.96986 / 3.50 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.163 Fit side-chains REVERT: M 25 LEU cc_start: 0.8766 (mp) cc_final: 0.8428 (mt) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.7861 time to fit residues: 52.1926 Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain N residue 6 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN B 4 ASN C 4 ASN E 4 ASN I 4 ASN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 ASN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.168750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.159251 restraints weight = 3953.483| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.72 r_work: 0.4144 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3240 Z= 0.130 Angle : 0.616 6.631 4365 Z= 0.305 Chirality : 0.043 0.097 480 Planarity : 0.003 0.017 555 Dihedral : 7.393 29.786 390 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.32 % Allowed : 34.78 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.16 (0.24), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.18), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 9 PHE 0.009 0.001 PHE B 23 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 3225) covalent geometry : angle 0.61667 / 0.31 ( 4335) SS BOND : bond 0.00151 / 0.09 ( 15) SS BOND : angle 0.58009 / 0.36 ( 30) hydrogen bonds : bond 0.01732 / 1.07 ( 42) hydrogen bonds : angle 4.95155 / 3.48 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.164 Fit side-chains REVERT: B 25 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8384 (mm) REVERT: G 9 ARG cc_start: 0.8267 (ttt90) cc_final: 0.6983 (ttp-170) REVERT: M 25 LEU cc_start: 0.8778 (mp) cc_final: 0.8443 (mt) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.7037 time to fit residues: 46.8128 Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain H residue 4 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 ASN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.169039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.159330 restraints weight = 3951.019| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.73 r_work: 0.4139 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3240 Z= 0.124 Angle : 0.614 6.864 4365 Z= 0.303 Chirality : 0.044 0.096 480 Planarity : 0.003 0.018 555 Dihedral : 7.346 29.335 390 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 1.74 % Allowed : 36.23 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.03 (0.25), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.19), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG K 9 PHE 0.009 0.001 PHE B 23 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 3225) covalent geometry : angle 0.61397 / 0.30 ( 4335) SS BOND : bond 0.00150 / 0.09 ( 15) SS BOND : angle 0.59615 / 0.37 ( 30) hydrogen bonds : bond 0.01911 / 1.23 ( 42) hydrogen bonds : angle 5.19521 / 3.63 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.075 Fit side-chains REVERT: L 25 LEU cc_start: 0.8850 (mp) cc_final: 0.8574 (mp) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.5860 time to fit residues: 37.7081 Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 6 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.0570 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.162170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.152419 restraints weight = 4033.121| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.79 r_work: 0.4077 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3240 Z= 0.166 Angle : 0.673 6.812 4365 Z= 0.333 Chirality : 0.044 0.096 480 Planarity : 0.003 0.018 555 Dihedral : 7.819 31.804 390 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 1.74 % Allowed : 36.81 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.90 (0.27), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.21), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 9 PHE 0.009 0.001 PHE B 23 HIS 0.004 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 3225) covalent geometry : angle 0.67266 / 0.33 ( 4335) SS BOND : bond 0.00234 / 0.14 ( 15) SS BOND : angle 0.70082 / 0.44 ( 30) hydrogen bonds : bond 0.02159 / 1.35 ( 42) hydrogen bonds : angle 5.21114 / 3.64 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.121 Fit side-chains REVERT: G 9 ARG cc_start: 0.8319 (ttt90) cc_final: 0.7091 (ttp-170) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 0.5880 time to fit residues: 38.4700 Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain H residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.167829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.158180 restraints weight = 3838.256| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.73 r_work: 0.4139 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3240 Z= 0.120 Angle : 0.627 7.247 4365 Z= 0.306 Chirality : 0.043 0.097 480 Planarity : 0.003 0.019 555 Dihedral : 7.521 31.176 390 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.16 % Allowed : 37.39 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.82 (0.28), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.21), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG O 9 PHE 0.010 0.001 PHE B 23 HIS 0.002 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 3225) covalent geometry : angle 0.62671 / 0.31 ( 4335) SS BOND : bond 0.00144 / 0.09 ( 15) SS BOND : angle 0.62946 / 0.39 ( 30) hydrogen bonds : bond 0.01980 / 1.22 ( 42) hydrogen bonds : angle 5.24332 / 3.66 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.075 Fit side-chains REVERT: G 9 ARG cc_start: 0.8212 (ttt90) cc_final: 0.7044 (ttp-170) REVERT: L 25 LEU cc_start: 0.8824 (mp) cc_final: 0.8594 (mp) outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.7321 time to fit residues: 44.7903 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain O residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN B 4 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.173340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.163559 restraints weight = 3890.022| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.71 r_work: 0.4176 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3240 Z= 0.101 Angle : 0.592 6.973 4365 Z= 0.288 Chirality : 0.043 0.096 480 Planarity : 0.003 0.033 555 Dihedral : 7.095 30.225 390 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.03 % Allowed : 36.81 % Favored : 61.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.67 (0.29), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.22), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG M 9 PHE 0.009 0.001 PHE J 23 HIS 0.002 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 3225) covalent geometry : angle 0.59222 / 0.29 ( 4335) SS BOND : bond 0.00116 / 0.07 ( 15) SS BOND : angle 0.52941 / 0.33 ( 30) hydrogen bonds : bond 0.01773 / 1.09 ( 42) hydrogen bonds : angle 5.10594 / 3.57 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.13 seconds wall clock time: 24 minutes 40.19 seconds (1480.19 seconds total)