Starting phenix.real_space_refine on Thu Jul 2 11:58:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.map" model { file = "/net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zxa_11516/07_2026/6zxa_11516.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Mg 21 5.21 5 S 35 5.16 5 C 6034 2.51 5 N 1127 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8442 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "B" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "D" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "E" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "F" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "G" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "H" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "J" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "K" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "L" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QS2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QSE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'QS2': 1, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'QS2': 1, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8442 At special positions: 0 Unit cell: (87.21, 87.21, 68.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 Mg 21 11.99 O 1225 8.00 N 1127 7.00 C 6034 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 360.3 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 54.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 34 through 55 Processing helix chain 'B' and resid 12 through 45 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 34 through 55 Processing helix chain 'D' and resid 12 through 45 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 34 through 55 Processing helix chain 'F' and resid 12 through 45 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 34 through 55 Processing helix chain 'H' and resid 12 through 45 Processing helix chain 'I' and resid 23 through 27 Processing helix chain 'I' and resid 34 through 55 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 23 through 27 Processing helix chain 'K' and resid 34 through 55 Processing helix chain 'L' and resid 12 through 45 Processing helix chain 'M' and resid 23 through 27 Processing helix chain 'M' and resid 34 through 55 Processing helix chain 'N' and resid 12 through 45 350 hydrogen bonds defined for protein. 1008 hydrogen bond angles 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: 0.91 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 2163 1.35 - 1.55: 6552 1.55 - 1.76: 7 1.76 - 1.96: 70 1.96 - 2.17: 84 Bond restraints: 8876 Sorted by residual: bond pdb=" C6 QS2 B 103 " pdb=" C7 QS2 B 103 " ideal model delta sigma weight residual 1.468 1.395 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C6 QS2 K 102 " pdb=" C7 QS2 K 102 " ideal model delta sigma weight residual 1.468 1.395 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C6 QS2 G 102 " pdb=" C7 QS2 G 102 " ideal model delta sigma weight residual 1.468 1.395 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C6 QS2 E 103 " pdb=" C7 QS2 E 103 " ideal model delta sigma weight residual 1.468 1.395 0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C6 QS2 M 103 " pdb=" C7 QS2 M 103 " ideal model delta sigma weight residual 1.468 1.396 0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11664 2.50 - 5.00: 572 5.00 - 7.50: 107 7.50 - 10.00: 26 10.00 - 12.50: 49 Bond angle restraints: 12418 Sorted by residual: angle pdb=" C ASN E 16 " pdb=" N HIS E 17 " pdb=" CA HIS E 17 " ideal model delta sigma weight residual 121.80 109.30 12.50 2.44e+00 1.68e-01 2.62e+01 angle pdb=" C ASN C 16 " pdb=" N HIS C 17 " pdb=" CA HIS C 17 " ideal model delta sigma weight residual 121.80 109.31 12.49 2.44e+00 1.68e-01 2.62e+01 angle pdb=" C ASN K 16 " pdb=" N HIS K 17 " pdb=" CA HIS K 17 " ideal model delta sigma weight residual 121.80 109.32 12.48 2.44e+00 1.68e-01 2.62e+01 angle pdb=" C ASN A 16 " pdb=" N HIS A 17 " pdb=" CA HIS A 17 " ideal model delta sigma weight residual 121.80 109.32 12.48 2.44e+00 1.68e-01 2.61e+01 angle pdb=" C ASN M 16 " pdb=" N HIS M 17 " pdb=" CA HIS M 17 " ideal model delta sigma weight residual 121.80 109.32 12.48 2.44e+00 1.68e-01 2.61e+01 ... (remaining 12413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.81: 3808 19.81 - 39.62: 434 39.62 - 59.44: 231 59.44 - 79.25: 49 79.25 - 99.06: 70 Dihedral angle restraints: 4592 sinusoidal: 2282 harmonic: 2310 Sorted by residual: dihedral pdb=" CA MET M 6 " pdb=" C MET M 6 " pdb=" N MET M 7 " pdb=" CA MET M 7 " ideal model delta harmonic sigma weight residual 180.00 144.13 35.87 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA MET C 6 " pdb=" C MET C 6 " pdb=" N MET C 7 " pdb=" CA MET C 7 " ideal model delta harmonic sigma weight residual 180.00 144.14 35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" CA MET K 6 " pdb=" C MET K 6 " pdb=" N MET K 7 " pdb=" CA MET K 7 " ideal model delta harmonic sigma weight residual 180.00 144.16 35.84 0 5.00e+00 4.00e-02 5.14e+01 ... (remaining 4589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1006 0.082 - 0.164: 107 0.164 - 0.245: 14 0.245 - 0.327: 7 0.327 - 0.408: 7 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CA HIS K 17 " pdb=" N HIS K 17 " pdb=" C HIS K 17 " pdb=" CB HIS K 17 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA HIS A 17 " pdb=" N HIS A 17 " pdb=" C HIS A 17 " pdb=" CB HIS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA HIS I 17 " pdb=" N HIS I 17 " pdb=" C HIS I 17 " pdb=" CB HIS I 17 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 1138 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 QS2 B 103 " -0.079 2.00e-02 2.50e+03 8.41e-02 7.08e+01 pdb=" C30 QS2 B 103 " 0.063 2.00e-02 2.50e+03 pdb=" C33 QS2 B 103 " 0.103 2.00e-02 2.50e+03 pdb=" C35 QS2 B 103 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 QS2 E 103 " 0.079 2.00e-02 2.50e+03 8.40e-02 7.06e+01 pdb=" C30 QS2 E 103 " -0.062 2.00e-02 2.50e+03 pdb=" C33 QS2 E 103 " -0.103 2.00e-02 2.50e+03 pdb=" C35 QS2 E 103 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 QS2 G 102 " 0.079 2.00e-02 2.50e+03 8.39e-02 7.04e+01 pdb=" C30 QS2 G 102 " -0.063 2.00e-02 2.50e+03 pdb=" C33 QS2 G 102 " -0.103 2.00e-02 2.50e+03 pdb=" C35 QS2 G 102 " 0.087 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2559 2.84 - 3.35: 7916 3.35 - 3.87: 16231 3.87 - 4.38: 18872 4.38 - 4.90: 28873 Nonbonded interactions: 74451 Sorted by model distance: nonbonded pdb=" O LYS K 23 " pdb=" OG1 THR K 26 " model vdw 2.324 3.040 nonbonded pdb=" O LYS C 23 " pdb=" OG1 THR C 26 " model vdw 2.324 3.040 nonbonded pdb=" O LYS M 23 " pdb=" OG1 THR M 26 " model vdw 2.324 3.040 nonbonded pdb=" O LYS A 23 " pdb=" OG1 THR A 26 " model vdw 2.325 3.040 nonbonded pdb=" O LYS I 23 " pdb=" OG1 THR I 26 " model vdw 2.325 3.040 ... (remaining 74446 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' and resid 2 through 70) selection = (chain 'C' and resid 2 through 70) selection = (chain 'E' and resid 2 through 70) selection = (chain 'G' and resid 2 through 70) selection = (chain 'I' and resid 2 through 70) selection = (chain 'K' and resid 2 through 70) selection = (chain 'M' and resid 2 through 70) } ncs_group { reference = (chain 'B' and (resid 5 through 48 or resid 102)) selection = (chain 'D' and (resid 5 through 48 or resid 102)) selection = (chain 'F' and (resid 5 through 48 or resid 102)) selection = (chain 'H' and (resid 5 through 48 or resid 102)) selection = (chain 'J' and (resid 5 through 48 or resid 102)) selection = (chain 'L' and (resid 5 through 48 or resid 102)) selection = (chain 'N' and (resid 5 through 48 or resid 102)) } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 13.890 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 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 : 0.025 0.802 8897 Z= 1.321 Angle : 1.396 12.496 12418 Z= 0.567 Chirality : 0.067 0.408 1141 Planarity : 0.012 0.084 1533 Dihedral : 24.899 99.061 3080 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 5.21 % Allowed : 11.46 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.92 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.27), residues: 763 helix: 1.68 (0.20), residues: 343 sheet: None (None), residues: 0 loop : -2.92 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 65 TYR 0.006 0.001 TYR K 58 PHE 0.030 0.005 PHE D 19 TRP 0.021 0.003 TRP M 33 HIS 0.022 0.004 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.45 ( 8876) covalent geometry : angle 1.39594 / 0.57 (12418) hydrogen bonds : bond 0.09978 / 6.97 ( 350) hydrogen bonds : angle 5.24649 / 3.61 ( 1008) Misc. bond : bond 0.47765 / 35.30 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.176 Fit side-chains REVERT: C 17 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6267 (t70) REVERT: M 17 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6374 (t70) outliers start: 35 outliers final: 17 residues processed: 155 average time/residue: 0.4208 time to fit residues: 70.0168 Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 17 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 64 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN ** L 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115154 restraints weight = 8402.362| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.11 r_work: 0.3049 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.170 8897 Z= 0.191 Angle : 1.128 10.229 12418 Z= 0.437 Chirality : 0.050 0.256 1141 Planarity : 0.007 0.061 1533 Dihedral : 23.811 89.891 1705 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 3.57 % Allowed : 14.58 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.29), residues: 763 helix: 2.89 (0.20), residues: 357 sheet: None (None), residues: 0 loop : -2.98 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 65 TYR 0.006 0.001 TYR I 58 PHE 0.024 0.003 PHE J 19 TRP 0.016 0.002 TRP K 33 HIS 0.012 0.002 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 8876) covalent geometry : angle 1.12763 / 0.44 (12418) hydrogen bonds : bond 0.06127 / 3.99 ( 350) hydrogen bonds : angle 4.55058 / 3.14 ( 1008) Misc. bond : bond 0.09510 / 7.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.272 Fit side-chains REVERT: I 7 MET cc_start: 0.7966 (tpp) cc_final: 0.7586 (tmm) outliers start: 24 outliers final: 11 residues processed: 132 average time/residue: 0.4727 time to fit residues: 67.3259 Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3525 r_free = 0.3525 target = 0.137880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113257 restraints weight = 8366.502| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.11 r_work: 0.3022 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 8897 Z= 0.208 Angle : 1.142 10.501 12418 Z= 0.441 Chirality : 0.053 0.292 1141 Planarity : 0.007 0.047 1533 Dihedral : 23.232 89.936 1685 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 4.32 % Allowed : 14.43 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.30), residues: 763 helix: 3.16 (0.21), residues: 357 sheet: None (None), residues: 0 loop : -3.03 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 65 TYR 0.005 0.001 TYR H 44 PHE 0.025 0.004 PHE D 19 TRP 0.014 0.002 TRP C 22 HIS 0.004 0.001 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 8876) covalent geometry : angle 1.14231 / 0.44 (12418) hydrogen bonds : bond 0.06365 / 4.16 ( 350) hydrogen bonds : angle 4.63058 / 3.20 ( 1008) Misc. bond : bond 0.08110 / 6.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.291 Fit side-chains outliers start: 29 outliers final: 10 residues processed: 129 average time/residue: 0.5045 time to fit residues: 69.8438 Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112529 restraints weight = 8618.248| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.13 r_work: 0.3018 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 8897 Z= 0.208 Angle : 1.140 10.385 12418 Z= 0.438 Chirality : 0.053 0.286 1141 Planarity : 0.007 0.047 1533 Dihedral : 22.933 89.819 1683 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 3.72 % Allowed : 15.77 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.30), residues: 763 helix: 3.23 (0.21), residues: 357 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG K 65 TYR 0.006 0.001 TYR B 44 PHE 0.026 0.004 PHE J 19 TRP 0.014 0.002 TRP C 22 HIS 0.005 0.001 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 8876) covalent geometry : angle 1.13977 / 0.44 (12418) hydrogen bonds : bond 0.06359 / 4.15 ( 350) hydrogen bonds : angle 4.62708 / 3.19 ( 1008) Misc. bond : bond 0.07306 / 5.55 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.312 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 118 average time/residue: 0.5275 time to fit residues: 66.7534 Evaluate side-chains 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3558 r_free = 0.3558 target = 0.139842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114603 restraints weight = 8581.044| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.13 r_work: 0.3048 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 8897 Z= 0.188 Angle : 1.090 10.372 12418 Z= 0.416 Chirality : 0.049 0.240 1141 Planarity : 0.006 0.044 1533 Dihedral : 22.231 89.749 1681 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 4.17 % Allowed : 15.33 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.29), residues: 763 helix: 2.55 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.82 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG K 65 TYR 0.006 0.001 TYR B 44 PHE 0.024 0.003 PHE D 19 TRP 0.014 0.002 TRP D 47 HIS 0.005 0.002 HIS H 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 8876) covalent geometry : angle 1.08992 / 0.42 (12418) hydrogen bonds : bond 0.06029 / 3.92 ( 350) hydrogen bonds : angle 4.54726 / 3.14 ( 1008) Misc. bond : bond 0.08005 / 6.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.301 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 114 average time/residue: 0.5643 time to fit residues: 68.6397 Evaluate side-chains 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3483 r_free = 0.3483 target = 0.134153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109672 restraints weight = 8514.603| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.12 r_work: 0.2976 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 8897 Z= 0.271 Angle : 1.252 11.077 12418 Z= 0.482 Chirality : 0.060 0.334 1141 Planarity : 0.008 0.057 1533 Dihedral : 24.031 89.986 1680 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 3.72 % Allowed : 15.33 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.30), residues: 763 helix: 3.45 (0.21), residues: 343 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG I 65 TYR 0.008 0.001 TYR H 44 PHE 0.031 0.004 PHE J 19 TRP 0.017 0.003 TRP C 22 HIS 0.010 0.002 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 ( 8876) covalent geometry : angle 1.25195 / 0.48 (12418) hydrogen bonds : bond 0.07023 / 4.62 ( 350) hydrogen bonds : angle 4.74150 / 3.28 ( 1008) Misc. bond : bond 0.05975 / 4.60 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: C 7 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7752 (tmm) REVERT: L 17 LYS cc_start: 0.8622 (mttp) cc_final: 0.8381 (mtmm) REVERT: M 7 MET cc_start: 0.7874 (tpt) cc_final: 0.7545 (tmm) outliers start: 25 outliers final: 9 residues processed: 126 average time/residue: 0.4934 time to fit residues: 66.8117 Evaluate side-chains 124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3535 r_free = 0.3535 target = 0.138156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113206 restraints weight = 8631.341| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.14 r_work: 0.3032 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 8897 Z= 0.200 Angle : 1.126 10.840 12418 Z= 0.431 Chirality : 0.051 0.261 1141 Planarity : 0.007 0.048 1533 Dihedral : 22.651 89.995 1680 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 3.72 % Allowed : 16.07 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.29), residues: 763 helix: 2.55 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 65 TYR 0.010 0.001 TYR H 44 PHE 0.025 0.004 PHE D 19 TRP 0.015 0.002 TRP H 47 HIS 0.010 0.002 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 8876) covalent geometry : angle 1.12555 / 0.43 (12418) hydrogen bonds : bond 0.06233 / 4.06 ( 350) hydrogen bonds : angle 4.60852 / 3.18 ( 1008) Misc. bond : bond 0.07783 / 5.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.287 Fit side-chains REVERT: M 14 THR cc_start: 0.7522 (p) cc_final: 0.7308 (t) outliers start: 25 outliers final: 12 residues processed: 118 average time/residue: 0.5828 time to fit residues: 73.2358 Evaluate side-chains 116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3540 r_free = 0.3540 target = 0.138626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113738 restraints weight = 8495.254| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.13 r_work: 0.3038 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 8897 Z= 0.198 Angle : 1.126 10.671 12418 Z= 0.438 Chirality : 0.050 0.239 1141 Planarity : 0.007 0.046 1533 Dihedral : 22.389 89.607 1680 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 2.53 % Allowed : 17.41 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 763 helix: 2.58 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 65 TYR 0.011 0.001 TYR H 44 PHE 0.024 0.003 PHE J 19 TRP 0.014 0.002 TRP H 47 HIS 0.009 0.002 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 8876) covalent geometry : angle 1.12638 / 0.44 (12418) hydrogen bonds : bond 0.06169 / 4.02 ( 350) hydrogen bonds : angle 4.57074 / 3.16 ( 1008) Misc. bond : bond 0.07687 / 5.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.288 Fit side-chains REVERT: A 17 HIS cc_start: 0.5071 (OUTLIER) cc_final: 0.4497 (m-70) REVERT: E 17 HIS cc_start: 0.5043 (OUTLIER) cc_final: 0.4681 (m-70) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.5789 time to fit residues: 65.8852 Evaluate side-chains 113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3529 r_free = 0.3529 target = 0.137726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112714 restraints weight = 8510.441| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.14 r_work: 0.3025 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 8897 Z= 0.209 Angle : 1.145 10.792 12418 Z= 0.446 Chirality : 0.052 0.252 1141 Planarity : 0.007 0.058 1533 Dihedral : 22.604 89.660 1680 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 2.23 % Allowed : 17.56 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.29), residues: 763 helix: 2.55 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 65 TYR 0.013 0.001 TYR H 44 PHE 0.026 0.004 PHE J 19 TRP 0.015 0.002 TRP G 22 HIS 0.009 0.002 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 ( 8876) covalent geometry : angle 1.14508 / 0.45 (12418) hydrogen bonds : bond 0.06315 / 4.12 ( 350) hydrogen bonds : angle 4.60812 / 3.18 ( 1008) Misc. bond : bond 0.07156 / 5.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.296 Fit side-chains REVERT: E 17 HIS cc_start: 0.5047 (OUTLIER) cc_final: 0.4719 (m-70) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.5221 time to fit residues: 59.0680 Evaluate side-chains 116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.135919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111257 restraints weight = 8518.303| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.13 r_work: 0.3004 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 8897 Z= 0.237 Angle : 1.209 11.346 12418 Z= 0.470 Chirality : 0.055 0.281 1141 Planarity : 0.007 0.059 1533 Dihedral : 23.276 89.985 1680 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 1.93 % Allowed : 18.01 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.30), residues: 763 helix: 2.50 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.59 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 65 TYR 0.016 0.002 TYR H 44 PHE 0.028 0.004 PHE J 19 TRP 0.016 0.002 TRP G 22 HIS 0.011 0.002 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 ( 8876) covalent geometry : angle 1.20853 / 0.47 (12418) hydrogen bonds : bond 0.06686 / 4.38 ( 350) hydrogen bonds : angle 4.69173 / 3.24 ( 1008) Misc. bond : bond 0.06337 / 4.81 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.310 Fit side-chains REVERT: E 17 HIS cc_start: 0.5156 (OUTLIER) cc_final: 0.4791 (m-70) REVERT: L 17 LYS cc_start: 0.8562 (mttp) cc_final: 0.8314 (mtmm) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.4783 time to fit residues: 56.7700 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** 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 = 0.3546 r_free = 0.3546 target = 0.138976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114009 restraints weight = 8489.008| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.14 r_work: 0.3044 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 8897 Z= 0.199 Angle : 1.132 10.972 12418 Z= 0.440 Chirality : 0.050 0.231 1141 Planarity : 0.007 0.049 1533 Dihedral : 22.241 89.830 1680 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 1.49 % Allowed : 19.20 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 763 helix: 2.57 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.55 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 65 TYR 0.017 0.002 TYR H 44 PHE 0.025 0.003 PHE D 19 TRP 0.014 0.002 TRP N 47 HIS 0.008 0.002 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 8876) covalent geometry : angle 1.13152 / 0.44 (12418) hydrogen bonds : bond 0.06170 / 4.01 ( 350) hydrogen bonds : angle 4.57713 / 3.16 ( 1008) Misc. bond : bond 0.07664 / 5.78 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3039.86 seconds wall clock time: 52 minutes 47.16 seconds (3167.16 seconds total)