Starting phenix.real_space_refine on Thu Jul 2 05:24:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hia_34813/07_2026/8hia_34813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hia_34813/07_2026/8hia_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hia_34813/07_2026/8hia_34813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hia_34813/07_2026/8hia_34813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hia_34813/07_2026/8hia_34813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hia_34813/07_2026/8hia_34813.map" } 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-dev-6108/lib/python3.11/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: 1.39, per 1000 atoms: 0.19 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: 0.59 Conformation dependent library (CDL) restraints added in 301.0 milliseconds 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: 0.48 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: 0.85 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: 2.170 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: 0.060 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0668 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 are 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/Z covalent geometry : bond 0.00129 / 0.07 ( 3580) covalent geometry : angle 0.35911 / 0.17 ( 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 : 0.011 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: 0.0420 time to fit residues: 0.1914 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=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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.122343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.106322 restraints weight = 2821.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.108614 restraints weight = 1359.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.110022 restraints weight = 875.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.110849 restraints weight = 680.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.110989 restraints weight = 596.447| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2326 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 22.060 480 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 are 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/Z covalent geometry : bond 0.01185 / 0.51 ( 3580) covalent geometry : angle 1.40676 / 0.84 ( 4920) *********************** REFINEMENT MACRO_CYCLE 2 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 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.012 Fit side-chains TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 3 average time/residue: 0.0399 time to fit residues: 0.1425 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 : 0.011 ------------------------------------------------------------------------------- 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: 0.0370 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 13 optimal weight: 0.0040 chunk 24 optimal weight: 5.9990 overall best weight: 0.1706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.179612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.150941 restraints weight = 1583.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.154280 restraints weight = 495.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.155594 restraints weight = 358.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.156197 restraints weight = 324.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.156186 restraints weight = 307.526| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3243 moved from start: 3.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3580 Z= 0.236 Angle : 0.789 4.514 4920 Z= 0.447 Chirality : 0.054 0.115 660 Planarity : 0.009 0.039 640 Dihedral : 7.089 20.219 480 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 are not related in a simple way. whole: -4.55 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 13 HIS 0.008 0.005 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 ( 3580) covalent geometry : angle 0.78919 / 0.45 ( 4920) *********************** REFINEMENT MACRO_CYCLE 3 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 6 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.014 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 6 average time/residue: 0.0249 time to fit residues: 0.1709 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.106250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.088871 restraints weight = 1874.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.092260 restraints weight = 1077.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.094481 restraints weight = 729.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.095750 restraints weight = 534.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.096324 restraints weight = 418.842| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2615 moved from start: 3.6023 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= 0.237 Angle : 0.730 5.185 4920 Z= 0.443 Chirality : 0.050 0.112 660 Planarity : 0.008 0.036 640 Dihedral : 6.679 18.611 480 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 32.50 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 are not related in a simple way. whole: -4.84 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG B 13 HIS 0.007 0.005 HIS S 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 ( 3580) covalent geometry : angle 0.72985 / 0.44 ( 4920) *********************** REFINEMENT MACRO_CYCLE 4 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 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.012 Fit side-chains TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0270 time to fit residues: 0.1315 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 : 0.011 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.099076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.082459 restraints weight = 2481.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.086038 restraints weight = 1468.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.088468 restraints weight = 988.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.090359 restraints weight = 718.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.091364 restraints weight = 533.174| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2685 moved from start: 3.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3580 Z= 0.312 Angle : 0.880 5.051 4920 Z= 0.470 Chirality : 0.063 0.157 660 Planarity : 0.007 0.024 640 Dihedral : 7.325 19.223 480 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 35.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.76 % Allowed : 9.52 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.43 (0.25), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.19), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 13 HIS 0.005 0.003 HIS T 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.31 ( 3580) covalent geometry : angle 0.87981 / 0.47 ( 4920) *********************** REFINEMENT MACRO_CYCLE 5 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 : 0.035 Fit side-chains TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0317 time to fit residues: 0.1858 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.137021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.114897 restraints weight = 1577.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.117983 restraints weight = 758.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.120116 restraints weight = 462.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.121467 restraints weight = 316.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.122442 restraints weight = 245.775| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3044 moved from start: 3.7338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3580 Z= 0.257 Angle : 0.731 4.519 4920 Z= 0.411 Chirality : 0.052 0.110 660 Planarity : 0.006 0.030 640 Dihedral : 7.329 21.441 480 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 31.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 are not related in a simple way. whole: -5.39 (0.24), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.18), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG K 13 HIS 0.002 0.001 HIS T 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 ( 3580) covalent geometry : angle 0.73054 / 0.41 ( 4920) *********************** REFINEMENT MACRO_CYCLE 6 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 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 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: 0.1338 time to fit residues: 0.9646 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.179637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.121233 restraints weight = 3467.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.129094 restraints weight = 1901.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.133590 restraints weight = 1512.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.134790 restraints weight = 1359.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.134944 restraints weight = 1300.695| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3977 moved from start: 3.8061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3580 Z= 0.315 Angle : 1.095 8.031 4920 Z= 0.608 Chirality : 0.060 0.130 660 Planarity : 0.022 0.115 640 Dihedral : 7.091 20.408 480 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 47.92 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 are not related in a simple way. whole: -4.97 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.004 ARG P 13 HIS 0.002 0.001 HIS D 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.32 ( 3580) covalent geometry : angle 1.09476 / 0.61 ( 4920) *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.012 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: 0.0391 time to fit residues: 0.2228 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 : 0.011 ------------------------------------------------------------------------------- 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: 7.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.171310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.109519 restraints weight = 2899.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.113440 restraints weight = 1899.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.115454 restraints weight = 1561.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.115869 restraints weight = 1425.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.116051 restraints weight = 1386.674| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3953 moved from start: 3.8327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 3580 Z= 0.221 Angle : 0.864 4.109 4920 Z= 0.483 Chirality : 0.057 0.145 660 Planarity : 0.020 0.107 640 Dihedral : 7.207 16.964 480 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 41.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 are not related in a simple way. whole: -5.39 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 13 HIS 0.002 0.002 HIS P 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 ( 3580) covalent geometry : angle 0.86424 / 0.48 ( 4920) *********************** REFINEMENT MACRO_CYCLE 8 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 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.017 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: 0.0363 time to fit residues: 0.1748 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 : 0.013 ------------------------------------------------------------------------------- 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: 7.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.169852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.110873 restraints weight = 3059.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.115284 restraints weight = 1805.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.117276 restraints weight = 1453.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.117768 restraints weight = 1330.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.117869 restraints weight = 1292.890| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3863 moved from start: 3.8525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3580 Z= 0.230 Angle : 0.812 3.868 4920 Z= 0.467 Chirality : 0.058 0.132 660 Planarity : 0.016 0.086 640 Dihedral : 6.917 16.675 480 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 47.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 are not related in a simple way. whole: -5.76 (0.25), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.19), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG P 13 HIS 0.003 0.002 HIS T 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 ( 3580) covalent geometry : angle 0.81181 / 0.47 ( 4920) *********************** REFINEMENT MACRO_CYCLE 9 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 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.014 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: 0.0300 time to fit residues: 0.1416 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 : 0.013 ------------------------------------------------------------------------------- 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: 0.4980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.154687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.106171 restraints weight = 1116.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.109068 restraints weight = 543.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.110669 restraints weight = 360.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.111509 restraints weight = 292.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.111911 restraints weight = 266.037| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3259 moved from start: 3.9381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3580 Z= 0.235 Angle : 0.875 4.693 4920 Z= 0.485 Chirality : 0.057 0.131 660 Planarity : 0.014 0.074 640 Dihedral : 7.823 16.686 480 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 43.19 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 are not related in a simple way. whole: -6.77 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.16 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 13 HIS 0.002 0.001 HIS L 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 ( 3580) covalent geometry : angle 0.87459 / 0.48 ( 4920) ********************** REFINEMENT MACRO_CYCLE 10 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 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. REVERT: T 9 MET cc_start: 0.4527 (mmp) cc_final: 0.3261 (mmt) outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0307 time to fit residues: 0.1474 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 : 0.011 ------------------------------------------------------------------------------- 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: 0.0470 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.159427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.111078 restraints weight = 1207.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.113662 restraints weight = 608.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.114898 restraints weight = 432.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.115343 restraints weight = 375.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.115343 restraints weight = 357.432| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3269 moved from start: 3.9546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3580 Z= 0.170 Angle : 0.752 3.976 4920 Z= 0.427 Chirality : 0.059 0.151 660 Planarity : 0.012 0.063 640 Dihedral : 7.226 14.656 480 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 33.75 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 are not related in a simple way. whole: -6.98 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG P 13 HIS 0.002 0.002 HIS L 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 3580) covalent geometry : angle 0.75183 / 0.43 ( 4920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 906.66 seconds wall clock time: 16 minutes 8.46 seconds (968.46 seconds total)