Starting phenix.real_space_refine on Fri Oct 23 04:46:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tiu_55970/10_2026/9tiu_55970.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tiu_55970/10_2026/9tiu_55970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tiu_55970/10_2026/9tiu_55970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tiu_55970/10_2026/9tiu_55970.map" model { file = "/net/cci-nas-00/data/ceres_data/9tiu_55970/10_2026/9tiu_55970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tiu_55970/10_2026/9tiu_55970.cif" } resolution = 3.68 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= 0.005 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: 5 Type Number sf(0) Gaussians S 25 5.16 5 C 2775 2.51 5 N 690 2.21 5 O 690 1.98 5 H 4175 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8355 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1671 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.24, per 1000 atoms: 0.15 Number of scatterers: 8355 At special positions: 0 Unit cell: (78.85, 79.68, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 O 690 8.00 N 690 7.00 C 2775 6.00 H 4175 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.71 Conformation dependent library (CDL) restraints added in 237.3 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1070 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.523A pdb=" N PHE A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 40 Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 74 through 105 removed outlier: 4.147A pdb=" N PHE A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.523A pdb=" N PHE B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 40 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 74 through 105 removed outlier: 4.147A pdb=" N PHE B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.522A pdb=" N PHE C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 40 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 74 through 105 removed outlier: 4.146A pdb=" N PHE C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 98 " --> pdb=" O MET C 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.523A pdb=" N PHE D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 40 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 74 through 105 removed outlier: 4.146A pdb=" N PHE D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.523A pdb=" N PHE E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 40 Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 74 through 105 removed outlier: 4.147A pdb=" N PHE E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 98 " --> pdb=" O MET E 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 136 355 hydrogen bonds defined for protein. 1065 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: 1.73 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4175 1.04 - 1.23: 38 1.23 - 1.43: 1637 1.43 - 1.62: 2510 1.62 - 1.82: 50 Bond restraints: 8410 Sorted by residual: bond pdb=" C PHE C 93 " pdb=" O PHE C 93 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 4.06e-01 bond pdb=" CG2 ILE A 96 " pdb="HG22 ILE A 96 " ideal model delta sigma weight residual 0.970 0.957 0.013 2.00e-02 2.50e+03 4.06e-01 bond pdb=" C PHE D 93 " pdb=" O PHE D 93 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 4.04e-01 bond pdb=" CG2 ILE B 96 " pdb="HG22 ILE B 96 " ideal model delta sigma weight residual 0.970 0.957 0.013 2.00e-02 2.50e+03 4.01e-01 bond pdb=" CG2 ILE D 96 " pdb="HG22 ILE D 96 " ideal model delta sigma weight residual 0.970 0.957 0.013 2.00e-02 2.50e+03 4.00e-01 ... (remaining 8405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.30: 15215 7.30 - 14.60: 0 14.60 - 21.90: 0 21.90 - 29.20: 0 29.20 - 36.50: 15 Bond angle restraints: 15230 Sorted by residual: angle pdb=" C ILE E 3 " pdb=" CA ILE E 3 " pdb=" HA ILE E 3 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ILE C 3 " pdb=" CA ILE C 3 " pdb=" HA ILE C 3 " ideal model delta sigma weight residual 109.00 72.52 36.48 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ILE A 3 " pdb=" CA ILE A 3 " pdb=" HA ILE A 3 " ideal model delta sigma weight residual 109.00 72.53 36.47 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ILE D 3 " pdb=" CA ILE D 3 " pdb=" HA ILE D 3 " ideal model delta sigma weight residual 109.00 72.53 36.47 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ILE B 3 " pdb=" CA ILE B 3 " pdb=" HA ILE B 3 " ideal model delta sigma weight residual 109.00 72.55 36.45 3.00e+00 1.11e-01 1.48e+02 ... (remaining 15225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 3395 15.85 - 31.71: 330 31.71 - 47.56: 130 47.56 - 63.41: 60 63.41 - 79.27: 5 Dihedral angle restraints: 3920 sinusoidal: 2000 harmonic: 1920 Sorted by residual: dihedral pdb=" C ILE C 3 " pdb=" N ILE C 3 " pdb=" CA ILE C 3 " pdb=" CB ILE C 3 " ideal model delta harmonic sigma weight residual -122.00 -133.44 11.44 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C ILE D 3 " pdb=" N ILE D 3 " pdb=" CA ILE D 3 " pdb=" CB ILE D 3 " ideal model delta harmonic sigma weight residual -122.00 -133.43 11.43 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C ILE A 3 " pdb=" N ILE A 3 " pdb=" CA ILE A 3 " pdb=" CB ILE A 3 " ideal model delta harmonic sigma weight residual -122.00 -133.42 11.42 0 2.50e+00 1.60e-01 2.09e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 649 0.066 - 0.132: 55 0.132 - 0.197: 1 0.197 - 0.263: 0 0.263 - 0.329: 5 Chirality restraints: 710 Sorted by residual: chirality pdb=" CA ILE C 3 " pdb=" N ILE C 3 " pdb=" C ILE C 3 " pdb=" CB ILE C 3 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ILE D 3 " pdb=" N ILE D 3 " pdb=" C ILE D 3 " pdb=" CB ILE D 3 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA ILE A 3 " pdb=" N ILE A 3 " pdb=" C ILE A 3 " pdb=" CB ILE A 3 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 707 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 57 " -0.004 2.00e-02 2.50e+03 3.98e-03 4.76e-01 pdb=" CG PHE E 57 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE E 57 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE E 57 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 57 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 57 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE E 57 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE E 57 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE E 57 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE E 57 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE E 57 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 57 " -0.004 2.00e-02 2.50e+03 3.96e-03 4.71e-01 pdb=" CG PHE B 57 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE B 57 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 57 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 57 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 57 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 57 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 57 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 57 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 57 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 57 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 57 " -0.004 2.00e-02 2.50e+03 3.87e-03 4.50e-01 pdb=" CG PHE A 57 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 57 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 57 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 57 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 57 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 57 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 57 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 57 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 57 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 57 " 0.000 2.00e-02 2.50e+03 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 991 2.25 - 2.83: 18143 2.83 - 3.42: 21194 3.42 - 4.01: 26409 4.01 - 4.60: 40127 Nonbonded interactions: 106864 Sorted by model distance: nonbonded pdb=" H ILE C 3 " pdb=" HA ILE C 3 " model vdw 1.658 1.816 nonbonded pdb=" H ILE A 3 " pdb=" HA ILE A 3 " model vdw 1.658 1.816 nonbonded pdb=" H ILE E 3 " pdb=" HA ILE E 3 " model vdw 1.658 1.816 nonbonded pdb=" H ILE D 3 " pdb=" HA ILE D 3 " model vdw 1.658 1.816 nonbonded pdb=" H ILE B 3 " pdb=" HA ILE B 3 " model vdw 1.659 1.816 ... (remaining 106859 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.500 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 : 0.003 0.027 4235 Z= 0.131 Angle : 0.594 6.610 5710 Z= 0.320 Chirality : 0.045 0.329 710 Planarity : 0.002 0.014 705 Dihedral : 16.352 79.267 1430 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 7.69 % Allowed : 22.31 % Favored : 70.00 % Cbeta Deviations : 0.93 % 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: 2.79 (0.36), residues: 545 helix: 2.59 (0.24), residues: 435 sheet: None (None), residues: 0 loop : -1.39 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.002 0.001 TYR E 75 PHE 0.012 0.001 PHE E 57 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4235) covalent geometry : angle 0.59402 / 0.32 ( 5710) hydrogen bonds : bond 0.13087 / 8.83 ( 355) hydrogen bonds : angle 4.39384 / 3.26 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7683 (t80) REVERT: B 39 ASP cc_start: 0.8402 (m-30) cc_final: 0.8153 (m-30) REVERT: B 54 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7833 (t80) REVERT: C 12 MET cc_start: 0.6691 (mmm) cc_final: 0.6414 (mmm) REVERT: C 54 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7584 (t80) REVERT: D 54 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7686 (t80) REVERT: E 9 GLU cc_start: 0.8222 (tp30) cc_final: 0.7799 (tt0) REVERT: E 39 ASP cc_start: 0.8384 (m-30) cc_final: 0.8165 (m-30) outliers start: 30 outliers final: 23 residues processed: 93 average time/residue: 0.0912 time to fit residues: 12.2518 Evaluate side-chains 86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [54, 24, 48, 26, 2, 16, 32, 31, 25, 50, 53] chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.112789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099353 restraints weight = 39197.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.102401 restraints weight = 18544.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104499 restraints weight = 10952.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.105713 restraints weight = 7274.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.106504 restraints weight = 5499.742| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4235 Z= 0.170 Angle : 0.584 5.890 5710 Z= 0.323 Chirality : 0.043 0.308 710 Planarity : 0.003 0.019 705 Dihedral : 12.106 80.527 631 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.21 % Allowed : 21.28 % Favored : 70.51 % Cbeta Deviations : 0.93 % 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: 2.46 (0.36), residues: 545 helix: 2.19 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -1.03 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 8 TYR 0.004 0.001 TYR C 75 PHE 0.009 0.001 PHE E 54 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 4235) covalent geometry : angle 0.58380 / 0.32 ( 5710) hydrogen bonds : bond 0.05273 / 3.61 ( 355) hydrogen bonds : angle 3.94733 / 2.91 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7744 (t80) REVERT: B 54 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7796 (t80) REVERT: C 54 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7586 (t80) REVERT: D 54 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7712 (t80) REVERT: E 39 ASP cc_start: 0.8474 (m-30) cc_final: 0.8273 (m-30) outliers start: 32 outliers final: 27 residues processed: 85 average time/residue: 0.0817 time to fit residues: 10.2218 Evaluate side-chains 89 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [33, 46, 29, 50, 26, 39, 54, 17, 20, 5, 6] chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.112314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099289 restraints weight = 39210.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.102322 restraints weight = 18436.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.104052 restraints weight = 10823.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.105553 restraints weight = 7569.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106540 restraints weight = 5390.174| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4235 Z= 0.158 Angle : 0.569 6.410 5710 Z= 0.310 Chirality : 0.043 0.312 710 Planarity : 0.003 0.017 705 Dihedral : 11.885 80.490 622 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 11.54 % Allowed : 19.23 % Favored : 69.23 % Cbeta Deviations : 0.93 % 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: 1.97 (0.36), residues: 545 helix: 1.91 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -1.54 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.004 0.001 TYR A 75 PHE 0.009 0.001 PHE C 7 HIS 0.002 0.001 HIS E 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 4235) covalent geometry : angle 0.56858 / 0.31 ( 5710) hydrogen bonds : bond 0.05020 / 3.47 ( 355) hydrogen bonds : angle 3.80672 / 2.81 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7707 (t80) REVERT: B 39 ASP cc_start: 0.8540 (m-30) cc_final: 0.8337 (m-30) REVERT: B 54 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 54 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7638 (t80) REVERT: D 54 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7697 (t80) REVERT: E 39 ASP cc_start: 0.8570 (m-30) cc_final: 0.8325 (m-30) outliers start: 45 outliers final: 37 residues processed: 98 average time/residue: 0.0858 time to fit residues: 12.2784 Evaluate side-chains 100 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [40, 37, 14, 9, 52, 54, 49, 18, 42, 31, 26] chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.102268 restraints weight = 38363.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.105407 restraints weight = 17767.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107475 restraints weight = 10271.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.108839 restraints weight = 6788.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109887 restraints weight = 5026.220| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4235 Z= 0.139 Angle : 0.572 5.978 5710 Z= 0.303 Chirality : 0.044 0.316 710 Planarity : 0.003 0.016 705 Dihedral : 11.706 80.128 620 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 12.05 % Allowed : 19.23 % Favored : 68.72 % Cbeta Deviations : 0.93 % 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: 2.51 (0.36), residues: 545 helix: 2.19 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.76 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.004 0.001 TYR C 75 PHE 0.008 0.001 PHE E 54 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 4235) covalent geometry : angle 0.57227 / 0.30 ( 5710) hydrogen bonds : bond 0.04743 / 3.28 ( 355) hydrogen bonds : angle 3.69094 / 2.72 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7669 (t80) REVERT: B 39 ASP cc_start: 0.8612 (m-30) cc_final: 0.8375 (m-30) REVERT: B 54 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7648 (t80) REVERT: C 54 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (t80) REVERT: D 54 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7660 (t80) REVERT: E 39 ASP cc_start: 0.8647 (m-30) cc_final: 0.8337 (m-30) outliers start: 47 outliers final: 34 residues processed: 99 average time/residue: 0.0851 time to fit residues: 12.4934 Evaluate side-chains 97 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [52, 25, 42, 50, 8, 31, 39, 14, 5, 33, 27] chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 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 = 0.3947 r_free = 0.3947 target = 0.115944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.102825 restraints weight = 38984.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.105946 restraints weight = 18414.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.107932 restraints weight = 10751.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.109329 restraints weight = 7254.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.110370 restraints weight = 5353.639| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4235 Z= 0.125 Angle : 0.582 6.726 5710 Z= 0.298 Chirality : 0.044 0.316 710 Planarity : 0.003 0.017 705 Dihedral : 11.445 79.152 617 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 12.05 % Allowed : 18.97 % Favored : 68.97 % Cbeta Deviations : 0.93 % 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: 2.57 (0.37), residues: 545 helix: 2.26 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.10 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 13 TYR 0.003 0.001 TYR E 75 PHE 0.007 0.001 PHE E 54 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 4235) covalent geometry : angle 0.58189 / 0.30 ( 5710) hydrogen bonds : bond 0.04424 / 3.07 ( 355) hydrogen bonds : angle 3.55022 / 2.61 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7653 (t80) REVERT: B 39 ASP cc_start: 0.8610 (m-30) cc_final: 0.8367 (m-30) REVERT: B 54 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7639 (t80) REVERT: C 54 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7606 (t80) REVERT: D 54 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7672 (t80) REVERT: E 39 ASP cc_start: 0.8592 (m-30) cc_final: 0.8309 (m-30) outliers start: 47 outliers final: 38 residues processed: 99 average time/residue: 0.0773 time to fit residues: 11.3159 Evaluate side-chains 101 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 59 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [16, 12, 30, 4, 6, 46, 43, 29, 45, 26, 0] chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.104824 restraints weight = 37848.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.107751 restraints weight = 18508.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.109621 restraints weight = 10997.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.110960 restraints weight = 7531.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.112028 restraints weight = 5539.495| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4235 Z= 0.131 Angle : 0.587 6.686 5710 Z= 0.299 Chirality : 0.044 0.316 710 Planarity : 0.003 0.019 705 Dihedral : 11.352 79.549 615 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 12.05 % Allowed : 18.97 % Favored : 68.97 % Cbeta Deviations : 0.93 % 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: 2.74 (0.36), residues: 545 helix: 2.36 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.75 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 8 TYR 0.004 0.001 TYR E 75 PHE 0.006 0.001 PHE E 7 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4235) covalent geometry : angle 0.58705 / 0.30 ( 5710) hydrogen bonds : bond 0.04351 / 3.02 ( 355) hydrogen bonds : angle 3.56694 / 2.63 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7695 (t80) REVERT: B 54 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7644 (t80) REVERT: C 54 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7598 (t80) REVERT: D 54 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7708 (t80) REVERT: E 39 ASP cc_start: 0.8577 (m-30) cc_final: 0.8330 (m-30) outliers start: 47 outliers final: 40 residues processed: 100 average time/residue: 0.0775 time to fit residues: 11.2849 Evaluate side-chains 103 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [10, 25, 8, 51, 49, 42, 14, 27, 0, 53, 13] chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.116811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.103789 restraints weight = 38681.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.106738 restraints weight = 18340.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108627 restraints weight = 10798.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110114 restraints weight = 7367.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.111229 restraints weight = 5282.726| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4235 Z= 0.170 Angle : 0.609 7.305 5710 Z= 0.319 Chirality : 0.044 0.315 710 Planarity : 0.003 0.020 705 Dihedral : 11.493 80.703 615 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 11.79 % Allowed : 20.26 % Favored : 67.95 % Cbeta Deviations : 0.93 % 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: 2.54 (0.36), residues: 545 helix: 2.21 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.80 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 8 TYR 0.005 0.001 TYR C 75 PHE 0.008 0.001 PHE E 54 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 4235) covalent geometry : angle 0.60886 / 0.32 ( 5710) hydrogen bonds : bond 0.04555 / 3.16 ( 355) hydrogen bonds : angle 3.75779 / 2.77 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 59 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 54 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7566 (t80) REVERT: C 54 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7590 (t80) REVERT: D 54 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7639 (t80) REVERT: E 39 ASP cc_start: 0.8694 (m-30) cc_final: 0.8417 (m-30) outliers start: 46 outliers final: 39 residues processed: 98 average time/residue: 0.0815 time to fit residues: 11.7937 Evaluate side-chains 102 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 59 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [11, 14, 52, 16, 0, 6, 8, 1, 36, 32, 35] chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 52 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.0000 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.2920 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.118331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.105303 restraints weight = 37789.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.108417 restraints weight = 17413.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.110584 restraints weight = 9978.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.112102 restraints weight = 6477.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.113110 restraints weight = 4519.575| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4235 Z= 0.119 Angle : 0.599 8.019 5710 Z= 0.294 Chirality : 0.045 0.318 710 Planarity : 0.003 0.023 705 Dihedral : 11.157 78.635 613 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 7.69 % Allowed : 24.10 % Favored : 68.21 % Cbeta Deviations : 0.93 % 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: 3.00 (0.37), residues: 545 helix: 2.56 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.83 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 13 TYR 0.003 0.001 TYR C 75 PHE 0.006 0.001 PHE C 57 HIS 0.001 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4235) covalent geometry : angle 0.59863 / 0.29 ( 5710) hydrogen bonds : bond 0.04130 / 2.88 ( 355) hydrogen bonds : angle 3.41271 / 2.52 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 54 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7602 (t80) REVERT: C 54 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7550 (t80) REVERT: D 54 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7655 (t80) REVERT: E 39 ASP cc_start: 0.8601 (m-30) cc_final: 0.8280 (m-30) outliers start: 30 outliers final: 24 residues processed: 83 average time/residue: 0.0866 time to fit residues: 10.6370 Evaluate side-chains 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [13, 14, 16, 32, 50, 37, 25, 22, 54, 17, 11] chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.116737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.103468 restraints weight = 38189.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.106620 restraints weight = 17674.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.108691 restraints weight = 10130.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.110227 restraints weight = 6706.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.111373 restraints weight = 4771.918| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4235 Z= 0.130 Angle : 0.604 5.992 5710 Z= 0.303 Chirality : 0.045 0.314 710 Planarity : 0.003 0.024 705 Dihedral : 11.211 79.337 613 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 10.00 % Allowed : 22.31 % Favored : 67.69 % Cbeta Deviations : 0.93 % 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: 2.97 (0.37), residues: 545 helix: 2.53 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.77 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 13 TYR 0.005 0.001 TYR B 75 PHE 0.008 0.001 PHE E 54 HIS 0.001 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4235) covalent geometry : angle 0.60389 / 0.30 ( 5710) hydrogen bonds : bond 0.04157 / 2.89 ( 355) hydrogen bonds : angle 3.49127 / 2.57 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7574 (t80) REVERT: B 54 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7528 (t80) REVERT: C 54 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7524 (t80) REVERT: D 54 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7597 (t80) REVERT: E 39 ASP cc_start: 0.8672 (m-30) cc_final: 0.8333 (m-30) outliers start: 39 outliers final: 32 residues processed: 92 average time/residue: 0.0811 time to fit residues: 10.8603 Evaluate side-chains 96 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [20, 15, 42, 8, 53, 9, 2, 11, 43, 24, 48] chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 0.1980 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.116485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.103177 restraints weight = 38566.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.106263 restraints weight = 17829.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.108214 restraints weight = 10287.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.109834 restraints weight = 6989.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.110932 restraints weight = 4934.495| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 4235 Z= 0.245 Angle : 1.143 59.198 5710 Z= 0.686 Chirality : 0.047 0.411 710 Planarity : 0.003 0.024 705 Dihedral : 11.226 79.349 613 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 10.51 % Allowed : 22.82 % Favored : 66.67 % Cbeta Deviations : 0.93 % 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: 2.93 (0.37), residues: 545 helix: 2.51 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.77 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.005 0.001 TYR B 75 PHE 0.008 0.001 PHE E 54 HIS 0.002 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 ( 4235) covalent geometry : angle 1.14309 / 0.69 ( 5710) hydrogen bonds : bond 0.04232 / 2.94 ( 355) hydrogen bonds : angle 3.50336 / 2.58 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 54 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7531 (t80) REVERT: C 54 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7531 (t80) REVERT: D 54 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7602 (t80) REVERT: E 39 ASP cc_start: 0.8671 (m-30) cc_final: 0.8381 (m-30) outliers start: 41 outliers final: 34 residues processed: 94 average time/residue: 0.0798 time to fit residues: 11.0734 Evaluate side-chains 97 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [3, 40, 22, 38, 12, 30, 23, 39, 14, 15, 52] chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 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 = 0.3938 r_free = 0.3938 target = 0.115524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.102509 restraints weight = 38466.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.105485 restraints weight = 18095.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107462 restraints weight = 10539.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108984 restraints weight = 7109.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.110027 restraints weight = 5078.062| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 4235 Z= 0.245 Angle : 1.143 59.198 5710 Z= 0.686 Chirality : 0.047 0.411 710 Planarity : 0.003 0.024 705 Dihedral : 11.226 79.349 613 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 9.74 % Allowed : 23.59 % Favored : 66.67 % Cbeta Deviations : 0.93 % 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: 2.93 (0.37), residues: 545 helix: 2.51 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -0.77 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.005 0.001 TYR B 75 PHE 0.008 0.001 PHE E 54 HIS 0.002 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 ( 4235) covalent geometry : angle 1.14309 / 0.69 ( 5710) hydrogen bonds : bond 0.04232 / 2.94 ( 355) hydrogen bonds : angle 3.50336 / 2.58 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1465.21 seconds wall clock time: 25 minutes 36.07 seconds (1536.07 seconds total)