Starting phenix.real_space_refine on Mon Feb 10 19:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iy7_35816/02_2025/8iy7_35816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iy7_35816/02_2025/8iy7_35816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iy7_35816/02_2025/8iy7_35816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iy7_35816/02_2025/8iy7_35816.map" model { file = "/net/cci-nas-00/data/ceres_data/8iy7_35816/02_2025/8iy7_35816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iy7_35816/02_2025/8iy7_35816.cif" } resolution = 3.71 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians I 48 10.91 5 C 864 2.51 5 N 264 2.21 5 O 288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1464 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 1.16, per 1000 atoms: 0.79 Number of scatterers: 1464 At special positions: 0 Unit cell: (112.88, 91.3, 27.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) I 48 52.95 O 288 8.00 N 264 7.00 C 864 6.00 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: 0.46 Conformation dependent library (CDL) restraints added in 89.1 milliseconds 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 192 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: 0.46 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: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 695 1.39 - 1.57: 745 1.57 - 1.74: 0 1.74 - 1.92: 0 1.92 - 2.09: 48 Bond restraints: 1488 Sorted by residual: bond pdb=" CZ PHI B 29 " pdb=" I PHI B 29 " ideal model delta sigma weight residual 2.106 1.979 0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CZ PHI L 29 " pdb=" I PHI L 29 " ideal model delta sigma weight residual 2.106 1.991 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" CZ PHI F 29 " pdb=" I PHI F 29 " ideal model delta sigma weight residual 2.106 1.995 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" CZ PHI W 29 " pdb=" I PHI W 29 " ideal model delta sigma weight residual 2.106 1.996 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" CZ PHI G 29 " pdb=" I PHI G 29 " ideal model delta sigma weight residual 2.106 2.001 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 1483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.70: 1852 7.70 - 15.40: 66 15.40 - 23.10: 31 23.10 - 30.80: 10 30.80 - 38.50: 9 Bond angle restraints: 1968 Sorted by residual: angle pdb=" N ASN N 25 " pdb=" CA ASN N 25 " pdb=" C ASN N 25 " ideal model delta sigma weight residual 107.88 72.98 34.90 1.41e+00 5.03e-01 6.13e+02 angle pdb=" C PHI W 23 " pdb=" CA PHI W 23 " pdb=" CB PHI W 23 " ideal model delta sigma weight residual 110.10 76.18 33.92 1.90e+00 2.77e-01 3.19e+02 angle pdb=" N ASN O 25 " pdb=" CA ASN O 25 " pdb=" C ASN O 25 " ideal model delta sigma weight residual 111.75 130.87 -19.12 1.28e+00 6.10e-01 2.23e+02 angle pdb=" C PHI V 23 " pdb=" CA PHI V 23 " pdb=" CB PHI V 23 " ideal model delta sigma weight residual 110.10 83.31 26.79 1.90e+00 2.77e-01 1.99e+02 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 111.71 127.89 -16.18 1.15e+00 7.56e-01 1.98e+02 ... (remaining 1963 not shown) Histogram of dihedral angle deviations from ideal: 0.04 - 17.24: 461 17.24 - 34.45: 62 34.45 - 51.65: 16 51.65 - 68.85: 11 68.85 - 86.06: 2 Dihedral angle restraints: 552 sinusoidal: 168 harmonic: 384 Sorted by residual: dihedral pdb=" C PHI V 23 " pdb=" N PHI V 23 " pdb=" CA PHI V 23 " pdb=" CB PHI V 23 " ideal model delta harmonic sigma weight residual -122.60 -88.87 -33.73 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" C PHI Q 23 " pdb=" N PHI Q 23 " pdb=" CA PHI Q 23 " pdb=" CB PHI Q 23 " ideal model delta harmonic sigma weight residual -122.60 -89.41 -33.19 0 2.50e+00 1.60e-01 1.76e+02 dihedral pdb=" C ASN G 25 " pdb=" N ASN G 25 " pdb=" CA ASN G 25 " pdb=" CB ASN G 25 " ideal model delta harmonic sigma weight residual -122.60 -154.89 32.29 0 2.50e+00 1.60e-01 1.67e+02 ... (remaining 549 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.289: 68 0.289 - 0.576: 22 0.576 - 0.864: 2 0.864 - 1.152: 2 1.152 - 1.439: 2 Chirality restraints: 96 Sorted by residual: chirality pdb=" CA PHI A 23 " pdb=" N PHI A 23 " pdb=" C PHI A 23 " pdb=" CB PHI A 23 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.18e+01 chirality pdb=" CA ASN G 25 " pdb=" N ASN G 25 " pdb=" C ASN G 25 " pdb=" CB ASN G 25 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.30 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" CA PHI B 23 " pdb=" N PHI B 23 " pdb=" C PHI B 23 " pdb=" CB PHI B 23 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.50e+01 ... (remaining 93 not shown) Planarity restraints: 312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHI W 29 " -0.031 2.00e-02 2.50e+03 1.58e-02 4.96e+00 pdb=" CG PHI W 29 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHI W 29 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHI W 29 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHI W 29 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHI W 29 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHI W 29 " 0.001 2.00e-02 2.50e+03 pdb=" I PHI W 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN O 27 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CG ASN O 27 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN O 27 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN O 27 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 27 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" CG ASN W 27 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN W 27 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN W 27 " 0.009 2.00e-02 2.50e+03 ... (remaining 309 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.40: 28 2.40 - 3.04: 863 3.04 - 3.68: 1471 3.68 - 4.32: 2175 4.32 - 4.96: 3084 Nonbonded interactions: 7621 Sorted by model distance: nonbonded pdb=" N ASN N 25 " pdb=" O ASN N 25 " model vdw 1.763 2.496 nonbonded pdb=" N PHI H 23 " pdb=" O PHI H 23 " model vdw 1.793 2.496 nonbonded pdb=" N PHI O 23 " pdb=" O PHI O 23 " model vdw 1.821 2.496 nonbonded pdb=" I PHI I 23 " pdb=" I PHI I 29 " model vdw 1.937 3.960 nonbonded pdb=" O GLY L 26 " pdb=" OD1 ASN L 27 " model vdw 1.955 3.040 ... (remaining 7616 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' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.480 Find NCS groups from input model: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3981 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 : 0.019 0.127 1488 Z= 0.983 Angle : 4.836 38.498 1968 Z= 2.291 Chirality : 0.352 1.439 96 Planarity : 0.005 0.017 312 Dihedral : 18.124 86.058 360 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 38.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 31.25 % 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: -5.43 (0.41), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.31), residues: 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0582 time to fit residues: 0.4787 Evaluate side-chains 2 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.223384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.207674 restraints weight = 5467.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.211460 restraints weight = 3052.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.212492 restraints weight = 1902.519| |-----------------------------------------------------------------------------| r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3939 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.148 1488 Z= 1.383 Angle : 3.229 17.704 1968 Z= 1.383 Chirality : 0.125 0.351 96 Planarity : 0.010 0.041 312 Dihedral : 25.098 87.081 264 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 45.94 Ramachandran Plot: Outliers : 2.78 % Allowed : 29.17 % Favored : 68.06 % Rotamer: Outliers : 10.42 % Allowed : 18.75 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.65 % 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: -6.60 (0.20), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.02 (0.15), residues: 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 2 time to evaluate : 0.100 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 7 average time/residue: 0.0621 time to fit residues: 0.6538 Evaluate side-chains 4 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.167325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.155937 restraints weight = 2011.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.159425 restraints weight = 657.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.160793 restraints weight = 256.416| |-----------------------------------------------------------------------------| r_work (final): 0.4929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3802 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.150 1488 Z= 1.311 Angle : 3.291 21.928 1968 Z= 1.389 Chirality : 0.116 0.297 96 Planarity : 0.010 0.044 312 Dihedral : 25.518 88.914 264 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 45.10 Ramachandran Plot: Outliers : 4.17 % Allowed : 36.11 % Favored : 59.72 % Rotamer: Outliers : 14.58 % Allowed : 25.00 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.21 % 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: -6.52 (0.39), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.29), residues: 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1 time to evaluate : 0.090 Fit side-chains REVERT: C 25 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8549 (m-40) outliers start: 7 outliers final: 5 residues processed: 8 average time/residue: 0.0515 time to fit residues: 0.6234 Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain R residue 25 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.150876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.141275 restraints weight = 2152.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.144085 restraints weight = 924.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.144771 restraints weight = 455.672| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3991 moved from start: 0.8550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.134 1488 Z= 1.290 Angle : 3.278 18.173 1968 Z= 1.372 Chirality : 0.113 0.272 96 Planarity : 0.009 0.038 312 Dihedral : 25.661 87.432 264 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 46.76 Ramachandran Plot: Outliers : 5.56 % Allowed : 37.50 % Favored : 56.94 % Rotamer: Outliers : 12.50 % Allowed : 27.08 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % 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: -6.48 (0.42), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.32), residues: 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1 time to evaluate : 0.093 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 7 average time/residue: 0.0574 time to fit residues: 0.6261 Evaluate side-chains 5 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain R residue 25 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 ASN R 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.150570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.140932 restraints weight = 2069.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.143741 restraints weight = 902.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.144715 restraints weight = 484.747| |-----------------------------------------------------------------------------| r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3946 moved from start: 0.9176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.134 1488 Z= 1.280 Angle : 3.326 18.623 1968 Z= 1.396 Chirality : 0.115 0.284 96 Planarity : 0.010 0.036 312 Dihedral : 25.692 87.021 264 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 44.30 Ramachandran Plot: Outliers : 6.94 % Allowed : 41.67 % Favored : 51.39 % Rotamer: Outliers : 16.67 % Allowed : 29.17 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.77 % 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: -6.48 (0.39), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.30), residues: 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1 time to evaluate : 0.101 Fit side-chains REVERT: W 25 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7332 (p0) outliers start: 8 outliers final: 6 residues processed: 9 average time/residue: 0.0619 time to fit residues: 0.7995 Evaluate side-chains 8 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain W residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.149544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.139795 restraints weight = 2144.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.142528 restraints weight = 894.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.142931 restraints weight = 489.730| |-----------------------------------------------------------------------------| r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3994 moved from start: 0.9762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.125 1488 Z= 1.274 Angle : 3.355 18.954 1968 Z= 1.417 Chirality : 0.117 0.363 96 Planarity : 0.010 0.036 312 Dihedral : 26.285 88.567 264 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 43.89 Ramachandran Plot: Outliers : 8.33 % Allowed : 37.50 % Favored : 54.17 % Rotamer: Outliers : 18.75 % Allowed : 25.00 % Favored : 56.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.77 % 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: -6.52 (0.36), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.27), residues: 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1 time to evaluate : 0.103 Fit side-chains REVERT: T 25 ASN cc_start: 0.8322 (p0) cc_final: 0.8109 (p0) REVERT: W 25 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7272 (p0) outliers start: 9 outliers final: 5 residues processed: 10 average time/residue: 0.0640 time to fit residues: 0.8954 Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain W residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.148298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.138120 restraints weight = 2082.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.140974 restraints weight = 869.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.140974 restraints weight = 438.692| |-----------------------------------------------------------------------------| r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4311 moved from start: 1.0118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.125 1488 Z= 1.263 Angle : 3.345 19.260 1968 Z= 1.401 Chirality : 0.111 0.274 96 Planarity : 0.010 0.037 312 Dihedral : 26.678 89.394 264 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 43.87 Ramachandran Plot: Outliers : 8.33 % Allowed : 37.50 % Favored : 54.17 % Rotamer: Outliers : 16.67 % Allowed : 29.17 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.25 % 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: -6.53 (0.37), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.28), residues: 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1 time to evaluate : 0.094 Fit side-chains REVERT: W 25 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7424 (p0) outliers start: 8 outliers final: 6 residues processed: 9 average time/residue: 0.0509 time to fit residues: 0.6972 Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 0 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain W residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.149679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.139363 restraints weight = 2152.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.141991 restraints weight = 896.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.143798 restraints weight = 460.612| |-----------------------------------------------------------------------------| r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4290 moved from start: 1.0462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.123 1488 Z= 1.257 Angle : 3.345 20.007 1968 Z= 1.400 Chirality : 0.108 0.272 96 Planarity : 0.009 0.036 312 Dihedral : 27.070 89.800 264 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 44.69 Ramachandran Plot: Outliers : 8.33 % Allowed : 36.11 % Favored : 55.56 % Rotamer: Outliers : 18.75 % Allowed : 27.08 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.25 % 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: -6.56 (0.38), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.99 (0.29), residues: 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1 time to evaluate : 0.076 Fit side-chains REVERT: T 25 ASN cc_start: 0.8238 (p0) cc_final: 0.7921 (p0) REVERT: W 25 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7448 (p0) outliers start: 9 outliers final: 7 residues processed: 10 average time/residue: 0.0464 time to fit residues: 0.6756 Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain W residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.147259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.138066 restraints weight = 2362.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.140791 restraints weight = 989.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.141757 restraints weight = 512.811| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4285 moved from start: 1.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.124 1488 Z= 1.252 Angle : 3.401 19.330 1968 Z= 1.418 Chirality : 0.108 0.266 96 Planarity : 0.010 0.036 312 Dihedral : 27.684 89.316 264 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 46.72 Ramachandran Plot: Outliers : 9.72 % Allowed : 38.89 % Favored : 51.39 % Rotamer: Outliers : 20.83 % Allowed : 27.08 % Favored : 52.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.77 % 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: -6.63 (0.34), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.05 (0.26), residues: 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.101 Fit side-chains REVERT: W 25 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7307 (p0) outliers start: 10 outliers final: 6 residues processed: 10 average time/residue: 0.0602 time to fit residues: 0.8525 Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 0 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain W residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.147654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.137905 restraints weight = 2356.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.140439 restraints weight = 1022.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.141180 restraints weight = 503.989| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4296 moved from start: 1.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.121 1488 Z= 1.251 Angle : 3.361 19.851 1968 Z= 1.402 Chirality : 0.108 0.302 96 Planarity : 0.010 0.036 312 Dihedral : 27.832 89.833 264 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 47.09 Ramachandran Plot: Outliers : 6.94 % Allowed : 40.28 % Favored : 52.78 % Rotamer: Outliers : 14.58 % Allowed : 31.25 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.29 % 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: -6.67 (0.28), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.08 (0.22), residues: 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 144 Ramachandran restraints generated. 72 Oldfield, 0 Emsley, 72 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1 time to evaluate : 0.087 Fit side-chains REVERT: T 25 ASN cc_start: 0.8381 (p0) cc_final: 0.8089 (p0) REVERT: W 25 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7433 (p0) outliers start: 7 outliers final: 6 residues processed: 8 average time/residue: 0.0585 time to fit residues: 0.6858 Evaluate side-chains 8 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain W residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.147491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.137743 restraints weight = 2373.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.140426 restraints weight = 989.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.142194 restraints weight = 500.188| |-----------------------------------------------------------------------------| r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4252 moved from start: 1.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.122 1488 Z= 1.250 Angle : 3.351 19.267 1968 Z= 1.401 Chirality : 0.108 0.297 96 Planarity : 0.010 0.036 312 Dihedral : 27.464 89.731 264 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 45.45 Ramachandran Plot: Outliers : 6.94 % Allowed : 41.67 % Favored : 51.39 % Rotamer: Outliers : 14.58 % Allowed : 31.25 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.77 % 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: -6.71 (0.26), residues: 72 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.11 (0.20), residues: 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 487.15 seconds wall clock time: 9 minutes 28.36 seconds (568.36 seconds total)