Starting phenix.real_space_refine on Fri Aug 22 18:41:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hia_34813/08_2025/8hia_34813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hia_34813/08_2025/8hia_34813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hia_34813/08_2025/8hia_34813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hia_34813/08_2025/8hia_34813.map" model { file = "/net/cci-nas-00/data/ceres_data/8hia_34813/08_2025/8hia_34813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hia_34813/08_2025/8hia_34813.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 2220 2.51 5 N 620 2.21 5 O 680 1.98 5 H 3660 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7200 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.30, per 1000 atoms: 0.18 Number of scatterers: 7200 At special positions: 0 Unit cell: (68.85, 114.75, 56.95, 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 20 16.00 O 680 8.00 N 620 7.00 C 2220 6.00 H 3660 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: 0.34 Conformation dependent library (CDL) restraints added in 175.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3660 1.03 - 1.23: 0 1.23 - 1.42: 1300 1.42 - 1.61: 2240 1.61 - 1.80: 40 Bond restraints: 7240 Sorted by residual: bond pdb=" N PRO N 2 " pdb=" CA PRO N 2 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 6.40e-01 bond pdb=" C GLU F 5 " pdb=" N PRO F 6 " ideal model delta sigma weight residual 1.326 1.337 -0.011 1.44e-02 4.82e+03 5.84e-01 bond pdb=" CA ARG F 13 " pdb=" C ARG F 13 " ideal model delta sigma weight residual 1.529 1.523 0.006 1.04e-02 9.25e+03 3.75e-01 bond pdb=" CA PRO N 2 " pdb=" C PRO N 2 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.42e-02 4.96e+03 3.32e-01 bond pdb=" CA VAL I 21 " pdb=" CB VAL I 21 " ideal model delta sigma weight residual 1.540 1.548 -0.008 1.36e-02 5.41e+03 3.23e-01 ... (remaining 7235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.70: 11911 0.70 - 1.40: 1178 1.40 - 2.09: 105 2.09 - 2.79: 30 2.79 - 3.49: 16 Bond angle restraints: 13240 Sorted by residual: angle pdb=" N ALA C 4 " pdb=" CA ALA C 4 " pdb=" C ALA C 4 " ideal model delta sigma weight residual 107.73 110.42 -2.69 1.34e+00 5.57e-01 4.03e+00 angle pdb=" N ALA G 4 " pdb=" CA ALA G 4 " pdb=" C ALA G 4 " ideal model delta sigma weight residual 110.80 107.48 3.32 2.13e+00 2.20e-01 2.43e+00 angle pdb=" N ALA D 10 " pdb=" CA ALA D 10 " pdb=" C ALA D 10 " ideal model delta sigma weight residual 108.46 110.73 -2.27 1.51e+00 4.39e-01 2.25e+00 angle pdb=" CA PRO N 2 " pdb=" C PRO N 2 " pdb=" O PRO N 2 " ideal model delta sigma weight residual 120.60 123.10 -2.50 1.82e+00 3.02e-01 1.89e+00 angle pdb=" CA PRO F 6 " pdb=" C PRO F 6 " pdb=" N ASP F 7 " ideal model delta sigma weight residual 115.12 116.81 -1.69 1.25e+00 6.40e-01 1.83e+00 ... (remaining 13235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3103 16.94 - 33.88: 185 33.88 - 50.82: 64 50.82 - 67.75: 20 67.75 - 84.69: 8 Dihedral angle restraints: 3380 sinusoidal: 1960 harmonic: 1420 Sorted by residual: dihedral pdb=" CB ARG S 13 " pdb=" CG ARG S 13 " pdb=" CD ARG S 13 " pdb=" NE ARG S 13 " ideal model delta sinusoidal sigma weight residual 180.00 120.04 59.96 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU J 1 " pdb=" CB GLU J 1 " pdb=" CG GLU J 1 " pdb=" CD GLU J 1 " ideal model delta sinusoidal sigma weight residual -180.00 -120.46 -59.54 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU Q 1 " pdb=" CB GLU Q 1 " pdb=" CG GLU Q 1 " pdb=" CD GLU Q 1 " ideal model delta sinusoidal sigma weight residual 180.00 -121.04 -58.96 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 343 0.024 - 0.048: 130 0.048 - 0.072: 48 0.072 - 0.096: 14 0.096 - 0.120: 125 Chirality restraints: 660 Sorted by residual: chirality pdb=" CA VAL S 17 " pdb=" N VAL S 17 " pdb=" C VAL S 17 " pdb=" CB VAL S 17 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA VAL D 17 " pdb=" N VAL D 17 " pdb=" C VAL D 17 " pdb=" CB VAL D 17 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA VAL I 14 " pdb=" N VAL I 14 " pdb=" C VAL I 14 " pdb=" CB VAL I 14 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 657 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 5 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO D 6 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 6 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 6 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 5 " 0.007 5.00e-02 4.00e+02 1.08e-02 1.87e-01 pdb=" N PRO L 6 " -0.019 5.00e-02 4.00e+02 pdb=" CA PRO L 6 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO L 6 " 0.006 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 5 " 0.001 2.00e-02 2.50e+03 2.85e-03 8.11e-02 pdb=" C GLU D 5 " -0.005 2.00e-02 2.50e+03 pdb=" O GLU D 5 " 0.002 2.00e-02 2.50e+03 pdb=" N PRO D 6 " 0.002 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 942 2.27 - 2.86: 15845 2.86 - 3.44: 15591 3.44 - 4.02: 20552 4.02 - 4.60: 29975 Nonbonded interactions: 82905 Sorted by model distance: nonbonded pdb=" OD1 ASP S 7 " pdb=" H MET S 9 " model vdw 1.694 2.450 nonbonded pdb=" HG1 THR G 19 " pdb=" OE1 GLN L 23 " model vdw 1.793 2.450 nonbonded pdb=" O ASN L 12 " pdb="HD22 ASN P 12 " model vdw 1.802 2.450 nonbonded pdb=" O ARG B 13 " pdb="HH11 ARG R 13 " model vdw 1.819 2.450 nonbonded pdb=" H1 GLU R 1 " pdb=" OE2 GLU S 1 " model vdw 1.834 2.450 ... (remaining 82900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set refine NCS operators NCS operators will be refined. 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: 1.590 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0837 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 : 0.001 0.012 3580 Z= 0.067 Angle : 0.359 3.489 4920 Z= 0.166 Chirality : 0.054 0.120 660 Planarity : 0.001 0.029 640 Dihedral : 15.833 84.693 1340 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.14 % Favored : 87.62 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.39 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 13 HIS 0.000 0.000 HIS R 16 Details of bonding type rmsd covalent geometry : bond 0.00129 ( 3580) covalent geometry : angle 0.35911 ( 4920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.009 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. REVERT: A 20 ASN cc_start: 0.5496 (m-40) cc_final: 0.4892 (p0) outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0251 time to fit residues: 0.1173 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.154039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.124772 restraints weight = 2783.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.131719 restraints weight = 1288.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.136654 restraints weight = 731.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.139949 restraints weight = 508.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.140632 restraints weight = 411.525| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3304 moved from start: 3.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.063 3580 Z= 0.513 Angle : 1.407 8.407 4920 Z= 0.836 Chirality : 0.077 0.221 660 Planarity : 0.006 0.019 640 Dihedral : 9.803 22.059 480 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 40.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.76 % Allowed : 19.05 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 13 HIS 0.008 0.006 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.01185 ( 3580) covalent geometry : angle 1.40675 ( 4920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.006 Fit side-chains TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0172 time to fit residues: 0.1043 Evaluate side-chains 2 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.166480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.130389 restraints weight = 1248.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.133162 restraints weight = 581.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.134691 restraints weight = 401.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.135353 restraints weight = 330.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.135751 restraints weight = 303.822| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2881 moved from start: 3.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 3580 Z= 0.239 Angle : 0.801 4.115 4920 Z= 0.460 Chirality : 0.050 0.117 660 Planarity : 0.014 0.054 640 Dihedral : 7.233 20.975 480 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 31.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.37 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 13 HIS 0.010 0.006 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 3580) covalent geometry : angle 0.80060 ( 4920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.011 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0298 time to fit residues: 0.1738 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.162830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.127380 restraints weight = 1205.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.129854 restraints weight = 514.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.131085 restraints weight = 335.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.131599 restraints weight = 280.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.131881 restraints weight = 263.389| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2882 moved from start: 3.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3580 Z= 0.212 Angle : 0.746 4.003 4920 Z= 0.434 Chirality : 0.050 0.116 660 Planarity : 0.008 0.035 640 Dihedral : 6.227 19.739 480 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG T 13 HIS 0.007 0.004 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 3580) covalent geometry : angle 0.74558 ( 4920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.010 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0190 time to fit residues: 0.0954 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.130633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.111011 restraints weight = 1759.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.113723 restraints weight = 743.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.115242 restraints weight = 432.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.116004 restraints weight = 312.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.116442 restraints weight = 264.008| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2740 moved from start: 3.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3580 Z= 0.213 Angle : 0.697 3.751 4920 Z= 0.403 Chirality : 0.049 0.125 660 Planarity : 0.007 0.026 640 Dihedral : 5.606 16.927 480 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.49 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 13 HIS 0.004 0.003 HIS P 16 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3580) covalent geometry : angle 0.69675 ( 4920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 7 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.007 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 0.1209 time to fit residues: 0.8634 Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.106667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.090730 restraints weight = 1685.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.093790 restraints weight = 870.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.096032 restraints weight = 532.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.097694 restraints weight = 354.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.098677 restraints weight = 253.064| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3114 moved from start: 3.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 3580 Z= 0.381 Angle : 0.961 4.318 4920 Z= 0.538 Chirality : 0.059 0.171 660 Planarity : 0.009 0.043 640 Dihedral : 8.318 21.898 480 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 37.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.29 (0.37), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 13 HIS 0.020 0.013 HIS T 16 Details of bonding type rmsd covalent geometry : bond 0.00858 ( 3580) covalent geometry : angle 0.96063 ( 4920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.007 Fit side-chains TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 0.0185 time to fit residues: 0.0523 Evaluate side-chains 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.124455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.104300 restraints weight = 1603.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.107681 restraints weight = 768.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.109554 restraints weight = 431.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.110953 restraints weight = 307.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.111627 restraints weight = 239.579| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2892 moved from start: 3.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3580 Z= 0.273 Angle : 0.763 3.698 4920 Z= 0.425 Chirality : 0.049 0.116 660 Planarity : 0.004 0.016 640 Dihedral : 7.385 15.713 480 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.41), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 13 HIS 0.013 0.008 HIS T 16 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 3580) covalent geometry : angle 0.76264 ( 4920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 6 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.007 Fit side-chains TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 6 average time/residue: 0.1466 time to fit residues: 0.8964 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.148220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.108183 restraints weight = 1528.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.111348 restraints weight = 741.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.112925 restraints weight = 495.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.114241 restraints weight = 402.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.114588 restraints weight = 353.590| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3676 moved from start: 3.8489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 3580 Z= 0.371 Angle : 1.169 8.216 4920 Z= 0.642 Chirality : 0.054 0.115 660 Planarity : 0.022 0.121 640 Dihedral : 8.564 24.549 480 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 39.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.63 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.005 ARG L 13 HIS 0.014 0.009 HIS T 16 Details of bonding type rmsd covalent geometry : bond 0.00888 ( 3580) covalent geometry : angle 1.16881 ( 4920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.011 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0395 time to fit residues: 0.1794 Evaluate side-chains 2 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.123092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.103264 restraints weight = 1757.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.105916 restraints weight = 835.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.107237 restraints weight = 535.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.108050 restraints weight = 422.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.108358 restraints weight = 364.400| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2896 moved from start: 3.8753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3580 Z= 0.222 Angle : 0.842 3.799 4920 Z= 0.477 Chirality : 0.056 0.132 660 Planarity : 0.019 0.106 640 Dihedral : 8.026 20.392 480 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 36.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.74 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG D 13 HIS 0.002 0.001 HIS C 16 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 3580) covalent geometry : angle 0.84235 ( 4920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 6 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.007 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 6 average time/residue: 0.1283 time to fit residues: 0.7945 Evaluate side-chains 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.122998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.099207 restraints weight = 1823.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.102021 restraints weight = 972.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.104006 restraints weight = 651.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.105261 restraints weight = 486.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.105900 restraints weight = 399.133| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3672 moved from start: 3.9354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3580 Z= 0.298 Angle : 0.954 5.092 4920 Z= 0.534 Chirality : 0.056 0.133 660 Planarity : 0.006 0.021 640 Dihedral : 9.303 20.887 480 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 37.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.46 (0.37), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG N 13 HIS 0.008 0.005 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 3580) covalent geometry : angle 0.95360 ( 4920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.011 Fit side-chains TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. REVERT: L 7 ASP cc_start: 0.7753 (p0) cc_final: 0.7297 (p0) outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.1837 time to fit residues: 0.9391 Evaluate side-chains 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.151727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.119887 restraints weight = 1927.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.121588 restraints weight = 1272.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.122397 restraints weight = 986.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.123082 restraints weight = 861.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.123100 restraints weight = 787.077| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3581 moved from start: 3.9205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 3580 Z= 0.347 Angle : 1.235 9.767 4920 Z= 0.666 Chirality : 0.066 0.227 660 Planarity : 0.043 0.239 640 Dihedral : 11.352 35.551 480 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 77.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.14 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.015 ARG K 13 HIS 0.020 0.013 HIS S 16 Details of bonding type rmsd covalent geometry : bond 0.00877 ( 3580) covalent geometry : angle 1.23459 ( 4920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 772.35 seconds wall clock time: 13 minutes 54.58 seconds (834.58 seconds total)