Starting phenix.real_space_refine on Wed Mar 5 14:17:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izz_35878/03_2025/8izz_35878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izz_35878/03_2025/8izz_35878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8izz_35878/03_2025/8izz_35878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izz_35878/03_2025/8izz_35878.map" model { file = "/net/cci-nas-00/data/ceres_data/8izz_35878/03_2025/8izz_35878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izz_35878/03_2025/8izz_35878.cif" } resolution = 3.75 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 44 10.91 5 C 792 2.51 5 N 242 2.21 5 O 264 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-5624/modules/chem_data/mon_lib" Total number of atoms: 1342 Number of models: 1 Model: "" Number of chains: 22 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: 0.95, per 1000 atoms: 0.71 Number of scatterers: 1342 At special positions: 0 Unit cell: (107.07, 86.32, 25.73, 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 44 52.95 O 264 8.00 N 242 7.00 C 792 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: 0.42 Conformation dependent library (CDL) restraints added in 77.7 milliseconds 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 176 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: 0.49 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: 654 1.39 - 1.57: 666 1.57 - 1.74: 0 1.74 - 1.92: 0 1.92 - 2.09: 44 Bond restraints: 1364 Sorted by residual: bond pdb=" CZ PHI H 29 " pdb=" I PHI H 29 " ideal model delta sigma weight residual 2.106 2.004 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" CZ PHI Q 23 " pdb=" I PHI Q 23 " ideal model delta sigma weight residual 2.106 2.004 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" CZ PHI R 29 " pdb=" I PHI R 29 " ideal model delta sigma weight residual 2.106 2.005 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CZ PHI F 29 " pdb=" I PHI F 29 " ideal model delta sigma weight residual 2.106 2.008 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CZ PHI E 23 " pdb=" I PHI E 23 " ideal model delta sigma weight residual 2.106 2.009 0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 1359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.25: 1713 7.25 - 14.50: 54 14.50 - 21.74: 23 21.74 - 28.99: 9 28.99 - 36.24: 5 Bond angle restraints: 1804 Sorted by residual: angle pdb=" N ASN X 25 " pdb=" CA ASN X 25 " pdb=" C ASN X 25 " ideal model delta sigma weight residual 113.97 145.55 -31.58 1.28e+00 6.10e-01 6.09e+02 angle pdb=" C ASN T 27 " pdb=" CA ASN T 27 " pdb=" CB ASN T 27 " ideal model delta sigma weight residual 111.22 75.73 35.49 1.72e+00 3.38e-01 4.26e+02 angle pdb=" N ASN A 25 " pdb=" CA ASN A 25 " pdb=" C ASN A 25 " ideal model delta sigma weight residual 108.24 84.80 23.44 1.32e+00 5.74e-01 3.15e+02 angle pdb=" N ASN L 25 " pdb=" CA ASN L 25 " pdb=" C ASN L 25 " ideal model delta sigma weight residual 111.75 133.88 -22.13 1.28e+00 6.10e-01 2.99e+02 angle pdb=" N ASN C 25 " pdb=" CA ASN C 25 " pdb=" C ASN C 25 " ideal model delta sigma weight residual 111.71 128.60 -16.89 1.15e+00 7.56e-01 2.16e+02 ... (remaining 1799 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.03: 425 15.03 - 30.06: 53 30.06 - 45.09: 17 45.09 - 60.12: 6 60.12 - 75.15: 5 Dihedral angle restraints: 506 sinusoidal: 154 harmonic: 352 Sorted by residual: dihedral pdb=" C ASN T 27 " pdb=" N ASN T 27 " pdb=" CA ASN T 27 " pdb=" CB ASN T 27 " ideal model delta harmonic sigma weight residual -122.60 -79.56 -43.04 0 2.50e+00 1.60e-01 2.96e+02 dihedral pdb=" C PHI L 29 " pdb=" N PHI L 29 " pdb=" CA PHI L 29 " pdb=" CB PHI L 29 " ideal model delta harmonic sigma weight residual -122.60 -89.31 -33.29 0 2.50e+00 1.60e-01 1.77e+02 dihedral pdb=" C ASN K 27 " pdb=" N ASN K 27 " pdb=" CA ASN K 27 " pdb=" CB ASN K 27 " ideal model delta harmonic sigma weight residual -122.60 -91.60 -31.00 0 2.50e+00 1.60e-01 1.54e+02 ... (remaining 503 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.315: 66 0.315 - 0.627: 17 0.627 - 0.939: 3 0.939 - 1.251: 0 1.251 - 1.564: 2 Chirality restraints: 88 Sorted by residual: chirality pdb=" CA ASN X 25 " pdb=" N ASN X 25 " pdb=" C ASN X 25 " pdb=" CB ASN X 25 " both_signs ideal model delta sigma weight residual False 2.51 0.95 1.56 2.00e-01 2.50e+01 6.11e+01 chirality pdb=" CA PHI X 23 " pdb=" N PHI X 23 " pdb=" C PHI X 23 " pdb=" CB PHI X 23 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA PHI J 23 " pdb=" N PHI J 23 " pdb=" C PHI J 23 " pdb=" CB PHI J 23 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 ... (remaining 85 not shown) Planarity restraints: 286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHI K 23 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C PHI K 23 " 0.042 2.00e-02 2.50e+03 pdb=" O PHI K 23 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY K 24 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 22 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C GLY I 22 " 0.025 2.00e-02 2.50e+03 pdb=" O GLY I 22 " -0.009 2.00e-02 2.50e+03 pdb=" N PHI I 23 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHI X 29 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C PHI X 29 " 0.024 2.00e-02 2.50e+03 pdb=" O PHI X 29 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY X 30 " -0.008 2.00e-02 2.50e+03 ... (remaining 283 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.47: 24 2.47 - 3.09: 874 3.09 - 3.71: 1396 3.71 - 4.34: 2018 4.34 - 4.96: 2896 Nonbonded interactions: 7208 Sorted by model distance: nonbonded pdb=" O ASN T 27 " pdb=" CB ASN T 27 " model vdw 1.847 2.752 nonbonded pdb=" O PHI M 29 " pdb=" OXT GLY M 30 " model vdw 2.009 3.040 nonbonded pdb=" N ASN A 25 " pdb=" O ASN A 25 " model vdw 2.044 2.496 nonbonded pdb=" O PHI U 23 " pdb=" CB PHI U 23 " model vdw 2.127 2.752 nonbonded pdb=" O PHI E 29 " pdb=" OXT GLY E 30 " model vdw 2.137 3.040 ... (remaining 7203 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 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' 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: 2.990 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.050 Find NCS groups from input model: 0.090 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3523 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 : 0.017 0.102 1364 Z= 0.862 Angle : 3.952 36.240 1804 Z= 2.007 Chirality : 0.344 1.564 88 Planarity : 0.004 0.025 286 Dihedral : 16.304 75.147 330 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 34.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 19.32 % 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: -5.84 (0.28), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.22), residues: 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0598 time to fit residues: 0.9674 Evaluate side-chains 7 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.136967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.124676 restraints weight = 1817.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.127687 restraints weight = 890.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.129896 restraints weight = 493.359| |-----------------------------------------------------------------------------| r_work (final): 0.4796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3889 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.143 1364 Z= 1.332 Angle : 3.472 21.319 1804 Z= 1.501 Chirality : 0.147 0.408 88 Planarity : 0.011 0.046 286 Dihedral : 24.729 89.252 242 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 34.47 Ramachandran Plot: Outliers : 4.55 % Allowed : 22.73 % Favored : 72.73 % Rotamer: Outliers : 11.36 % Allowed : 27.27 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.41 % 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: -6.21 (0.45), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.34), residues: 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.091 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.0595 time to fit residues: 0.4770 Evaluate side-chains 3 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: I 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.150094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.136804 restraints weight = 1787.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.139603 restraints weight = 894.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.141927 restraints weight = 584.146| |-----------------------------------------------------------------------------| r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4024 moved from start: 1.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.116 1364 Z= 1.203 Angle : 3.345 19.772 1804 Z= 1.456 Chirality : 0.138 0.366 88 Planarity : 0.011 0.038 286 Dihedral : 25.768 76.907 242 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 38.05 Ramachandran Plot: Outliers : 4.55 % Allowed : 27.27 % Favored : 68.18 % Rotamer: Outliers : 22.73 % Allowed : 25.00 % Favored : 52.27 % Cbeta Deviations : 2.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.39 % 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: -6.72 (0.15), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.12 (0.11), residues: 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.094 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 10 average time/residue: 0.0616 time to fit residues: 0.8605 Evaluate side-chains 6 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 0 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 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: ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.151186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.137582 restraints weight = 1744.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.140327 restraints weight = 947.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.142198 restraints weight = 607.070| |-----------------------------------------------------------------------------| r_work (final): 0.4858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3609 moved from start: 1.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.119 1364 Z= 1.184 Angle : 3.353 19.414 1804 Z= 1.443 Chirality : 0.135 0.376 88 Planarity : 0.011 0.042 286 Dihedral : 25.998 87.867 242 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 37.55 Ramachandran Plot: Outliers : 1.52 % Allowed : 40.91 % Favored : 57.58 % Rotamer: Outliers : 22.73 % Allowed : 29.55 % Favored : 47.73 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.52 % 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: -6.81 (0.15), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.18 (0.11), residues: 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.095 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 10 average time/residue: 0.0604 time to fit residues: 0.8495 Evaluate side-chains 6 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 0 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 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: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.150232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.136519 restraints weight = 1709.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.139538 restraints weight = 940.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.141144 restraints weight = 576.368| |-----------------------------------------------------------------------------| r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3661 moved from start: 1.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.123 1364 Z= 1.166 Angle : 3.380 20.561 1804 Z= 1.458 Chirality : 0.136 0.418 88 Planarity : 0.011 0.039 286 Dihedral : 25.262 81.184 242 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 33.09 Ramachandran Plot: Outliers : 1.52 % Allowed : 51.52 % Favored : 46.97 % Rotamer: Outliers : 20.45 % Allowed : 31.82 % Favored : 47.73 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.39 % 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: -6.98 (0.14), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.11), residues: 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.092 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 9 average time/residue: 0.0601 time to fit residues: 0.7647 Evaluate side-chains 7 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 0 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 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: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.134658 restraints weight = 1728.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.137681 restraints weight = 950.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.138936 restraints weight = 610.599| |-----------------------------------------------------------------------------| r_work (final): 0.4891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4002 moved from start: 1.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.121 1364 Z= 1.167 Angle : 3.396 20.998 1804 Z= 1.474 Chirality : 0.139 0.458 88 Planarity : 0.011 0.039 286 Dihedral : 25.580 80.276 242 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 37.53 Ramachandran Plot: Outliers : 3.03 % Allowed : 46.97 % Favored : 50.00 % Rotamer: Outliers : 22.73 % Allowed : 29.55 % Favored : 47.73 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.09 % 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: -6.96 (0.13), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.30 (0.10), residues: 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.091 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 10 average time/residue: 0.0580 time to fit residues: 0.8162 Evaluate side-chains 10 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.153823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.139296 restraints weight = 1769.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.142800 restraints weight = 952.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.145000 restraints weight = 548.481| |-----------------------------------------------------------------------------| r_work (final): 0.4935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4159 moved from start: 1.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.122 1364 Z= 1.177 Angle : 3.402 21.225 1804 Z= 1.482 Chirality : 0.139 0.401 88 Planarity : 0.011 0.043 286 Dihedral : 26.250 80.689 242 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 38.01 Ramachandran Plot: Outliers : 3.03 % Allowed : 51.52 % Favored : 45.45 % Rotamer: Outliers : 27.27 % Allowed : 20.45 % Favored : 52.27 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.66 % 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: -6.95 (0.13), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.10), residues: 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 0 time to evaluate : 0.090 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 12 average time/residue: 0.0555 time to fit residues: 0.9145 Evaluate side-chains 9 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.151465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.137817 restraints weight = 1761.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.141046 restraints weight = 908.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.143164 restraints weight = 563.042| |-----------------------------------------------------------------------------| r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4155 moved from start: 1.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.124 1364 Z= 1.171 Angle : 3.391 21.208 1804 Z= 1.477 Chirality : 0.138 0.426 88 Planarity : 0.011 0.042 286 Dihedral : 26.318 80.469 242 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 35.75 Ramachandran Plot: Outliers : 3.03 % Allowed : 48.48 % Favored : 48.48 % Rotamer: Outliers : 27.27 % Allowed : 20.45 % Favored : 52.27 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.52 % 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 (0.13), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.10), residues: 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 0 time to evaluate : 0.095 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 12 average time/residue: 0.0585 time to fit residues: 0.9599 Evaluate side-chains 9 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.126697 restraints weight = 1742.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.129822 restraints weight = 900.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.131468 restraints weight = 490.378| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3835 moved from start: 1.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.127 1364 Z= 1.172 Angle : 3.408 21.388 1804 Z= 1.481 Chirality : 0.138 0.412 88 Planarity : 0.011 0.041 286 Dihedral : 26.709 83.123 242 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 37.55 Ramachandran Plot: Outliers : 3.03 % Allowed : 54.55 % Favored : 42.42 % Rotamer: Outliers : 25.00 % Allowed : 20.45 % Favored : 54.55 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.66 % 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 (0.14), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.30 (0.11), residues: 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 0 time to evaluate : 0.091 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 11 average time/residue: 0.0574 time to fit residues: 0.8695 Evaluate side-chains 10 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain T 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: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.138760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.126556 restraints weight = 1873.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.129242 restraints weight = 895.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.131645 restraints weight = 507.577| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3808 moved from start: 1.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.191 1364 Z= 1.229 Angle : 3.891 59.197 1804 Z= 1.879 Chirality : 0.139 0.411 88 Planarity : 0.014 0.118 286 Dihedral : 26.700 82.890 242 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 38.00 Ramachandran Plot: Outliers : 3.03 % Allowed : 53.03 % Favored : 43.94 % Rotamer: Outliers : 25.00 % Allowed : 20.45 % Favored : 54.55 % Cbeta Deviations : 2.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.66 % 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 (0.14), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.10), residues: 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 132 Ramachandran restraints generated. 66 Oldfield, 0 Emsley, 66 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 0 time to evaluate : 0.088 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 11 average time/residue: 0.0558 time to fit residues: 0.8512 Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 0 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain T 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: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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 = 0.4700 r_free = 0.4700 target = 0.138996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.126306 restraints weight = 1903.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.129340 restraints weight = 903.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.131281 restraints weight = 505.468| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3832 moved from start: 1.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.191 1364 Z= 1.229 Angle : 3.891 59.197 1804 Z= 1.879 Chirality : 0.139 0.411 88 Planarity : 0.014 0.118 286 Dihedral : 26.700 82.890 242 Min Nonbonded Distance : 1.412 Molprobity Statistics. All-atom Clashscore : 37.55 Ramachandran Plot: Outliers : 3.03 % Allowed : 53.03 % Favored : 43.94 % Rotamer: Outliers : 18.18 % Allowed : 25.00 % Favored : 56.82 % Cbeta Deviations : 2.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.66 % 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 (0.14), residues: 66 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.10), residues: 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 466.94 seconds wall clock time: 8 minutes 48.33 seconds (528.33 seconds total)