Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 13:50:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hia_34813/10_2023/8hia_34813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hia_34813/10_2023/8hia_34813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hia_34813/10_2023/8hia_34813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hia_34813/10_2023/8hia_34813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hia_34813/10_2023/8hia_34813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hia_34813/10_2023/8hia_34813.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/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: 3.36, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 4.55 Conformation dependent library (CDL) restraints added in 501.7 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: 0.66 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: 4.78 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: 100.85 - 106.93: 195 106.93 - 113.01: 9282 113.01 - 119.10: 1265 119.10 - 125.18: 2318 125.18 - 131.26: 180 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: 2665 16.94 - 33.88: 128 33.88 - 50.82: 59 50.82 - 67.75: 20 67.75 - 84.69: 8 Dihedral angle restraints: 2880 sinusoidal: 1460 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 2877 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 1.850 nonbonded pdb=" HG1 THR G 19 " pdb=" OE1 GLN L 23 " model vdw 1.793 1.850 nonbonded pdb=" O ASN L 12 " pdb="HD22 ASN P 12 " model vdw 1.802 1.850 nonbonded pdb=" O ARG B 13 " pdb="HH11 ARG R 13 " model vdw 1.819 1.850 nonbonded pdb=" H1 GLU R 1 " pdb=" OE2 GLU S 1 " model vdw 1.834 1.850 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.120 Extract box with map and model: 5.660 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.640 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 3580 Z= 0.067 Angle : 0.359 3.489 4920 Z= 0.166 Chirality : 0.054 0.120 660 Planarity : 0.001 0.029 640 Dihedral : 15.833 84.693 1340 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.14 % Favored : 87.62 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.22), residues: 420 *********************** 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 fitting. rotamer outliers: 1 poor density : 4 time to evaluate : 0.034 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.1227 time to fit residues: 0.5580 Evaluate side-chains 3 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.033 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0070 time to fit residues: 0.0505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.0050 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.0770 chunk 23 optimal weight: 0.0040 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 overall best weight: 0.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0840 moved from start: 3.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.054 3580 Z= 0.431 Angle : 1.296 8.636 4920 Z= 0.760 Chirality : 0.073 0.215 660 Planarity : 0.005 0.010 640 Dihedral : 10.647 35.193 480 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 43.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.52 % Allowed : 9.52 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.25), residues: 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3 time to evaluate : 0.035 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 4 average time/residue: 0.0898 time to fit residues: 0.4271 Evaluate side-chains 5 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3 time to evaluate : 0.032 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0119 time to fit residues: 0.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0921 moved from start: 3.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3580 Z= 0.293 Angle : 0.823 4.498 4920 Z= 0.473 Chirality : 0.050 0.124 660 Planarity : 0.005 0.018 640 Dihedral : 8.628 23.080 480 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 40.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.26), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 4 time to evaluate : 0.033 Fit side-chains revert: symmetry clash 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: 0.0900 time to fit residues: 0.5279 Evaluate side-chains 4 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.032 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0077 time to fit residues: 0.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0891 moved from start: 3.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3580 Z= 0.288 Angle : 0.807 4.610 4920 Z= 0.467 Chirality : 0.050 0.116 660 Planarity : 0.006 0.026 640 Dihedral : 6.823 18.507 480 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 37.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.23), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 3 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.029 Fit side-chains revert: symmetry clash 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: 0.1129 time to fit residues: 0.3938 Evaluate side-chains 2 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1 time to evaluate : 0.028 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0067 time to fit residues: 0.0436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0792 moved from start: 3.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 3580 Z= 0.182 Angle : 0.658 4.305 4920 Z= 0.381 Chirality : 0.050 0.117 660 Planarity : 0.006 0.023 640 Dihedral : 6.560 22.075 480 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 28.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.22), residues: 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 2 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1 time to evaluate : 0.033 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 0.0906 time to fit residues: 0.2401 Evaluate side-chains 2 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1 time to evaluate : 0.032 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0073 time to fit residues: 0.0514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.0970 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0803 moved from start: 3.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3580 Z= 0.195 Angle : 0.665 4.015 4920 Z= 0.379 Chirality : 0.051 0.121 660 Planarity : 0.006 0.025 640 Dihedral : 6.834 22.690 480 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 28.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.72 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.21), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 3 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.028 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 0.0807 time to fit residues: 0.2132 Evaluate side-chains 3 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.028 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0068 time to fit residues: 0.0442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0822 moved from start: 3.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3580 Z= 0.197 Angle : 0.677 4.021 4920 Z= 0.389 Chirality : 0.050 0.102 660 Planarity : 0.008 0.040 640 Dihedral : 6.378 22.357 480 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 29.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.07 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.17), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 3 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.029 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 0.0829 time to fit residues: 0.2259 Evaluate side-chains 3 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.031 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0072 time to fit residues: 0.0485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0834 moved from start: 3.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3580 Z= 0.205 Angle : 0.672 3.960 4920 Z= 0.384 Chirality : 0.050 0.109 660 Planarity : 0.008 0.039 640 Dihedral : 6.676 23.645 480 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 34.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.46 (0.19), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.92 (0.15), residues: 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.032 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: 0.0892 time to fit residues: 0.4209 Evaluate side-chains 4 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.031 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0071 time to fit residues: 0.0486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0851 moved from start: 3.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 3580 Z= 0.257 Angle : 0.867 4.871 4920 Z= 0.483 Chirality : 0.054 0.145 660 Planarity : 0.007 0.030 640 Dihedral : 6.904 24.949 480 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 44.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.84 (0.19), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.21 (0.15), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.032 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: 0.0810 time to fit residues: 0.3887 Evaluate side-chains 4 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.031 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0070 time to fit residues: 0.0494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0823 moved from start: 3.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3580 Z= 0.227 Angle : 0.853 5.554 4920 Z= 0.464 Chirality : 0.056 0.142 660 Planarity : 0.007 0.035 640 Dihedral : 6.987 24.972 480 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 43.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.97 (0.20), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.15), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3 time to evaluate : 0.037 Fit side-chains TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.5227 time to fit residues: 2.1530 Evaluate side-chains 2 residues out of total 21 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1 time to evaluate : 0.033 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0075 time to fit residues: 0.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.105479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.096841 restraints weight = 3228.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.098904 restraints weight = 1755.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.100203 restraints weight = 1048.855| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2314 moved from start: 3.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3580 Z= 0.238 Angle : 0.834 4.258 4920 Z= 0.472 Chirality : 0.054 0.118 660 Planarity : 0.004 0.011 640 Dihedral : 7.851 25.171 480 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 41.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.09 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.40 (0.16), residues: 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.12 seconds wall clock time: 31 minutes 39.06 seconds (1899.06 seconds total)